Is it true that John MacArthur has reversed his position on the eternal Sonship of Christ?

Yes.
Here's a statement from John about his views on that issue.

Near the end of his life, Augustine of Hippo meticulously reviewed everything he had ever published. He wrote an entire catalogue of his own works, a painstakingly annotated bibliography with hundreds of revisions and amendments to correct flaws he saw in his own earlier material. The book, titled Retractationes, is powerful evidence of Augustine's humility and zeal for truth. Not one of his earlier publications escaped the more mature theologian's scrutiny. And Augustine was as bold in recanting the errors he perceived in his own work as he had been in refuting the heresies of his theological adversaries. Because he reviewed his works in chronological order, Retractationes is a wonderful memoir of Augustine's relentless, lifelong pursuit of spiritual maturity and theological precision. His forthrightness in addressing his own shortcomings is a good example of why Augustine is esteemed as a rare model of both godliness and scholarship.

I've often wished for the opportunity to review and amend all my own published material, but I doubt I'll ever have the time or the energy to undertake the task. In this day of electronic recordings, my "published" material includes not just the books I have written but also nearly every sermon I have ever preached—about 3,000 of them so far. It's far too much material to be able to critique exhaustively the way I wish I could.

Not that I would make sweeping or wholesale revisions. Throughout my ministry, my theological perspective has remained fundamentally unchanged. The basic doctrinal statement I subscribe to today is the same one I affirmed when I was ordained to the ministry almost 40 years ago. I am not someone whose convictions are easily malleable. I trust I am not a reed shaken in the wind, or the kind of person who is naively tossed about by various winds of doctrine.

But at the same time, I do not want to be resistant to growth and correction, especially when my comprehension of Scripture can be sharpened. If more precise understanding on an important point of doctrine demands a change in my thinking—even if it means amending or correcting already-published material—I want to be willing to make the necessary changes.

I have made many such revisions over the years, often taking measures to delete erroneous or confusing statements from my own tapes, and sometimes even preaching again through portions of Scripture with a better understanding of the text. Whenever I have changed my opinion on any significant doctrinal issue, I have sought to make my change of opinion, and the reasons for it, as clear as possible.

To that end, I want to state publicly that I have abandoned the doctrine of "incarnational sonship." Careful study and reflection have brought me to understand that Scripture does indeed present the relationship between God the Father and Christ the Son as an eternal Father-Son relationship. I no longer regard Christ's sonship as a role He assumed in His incarnation.

My earlier position arose out of my study of Hebrews 1:5, which appears to speak of the Father's begetting the Son as an event that takes place at a point in time: "This day have I begotten thee"; "I will be to him a Father, and he shall be to me a Son" (emphasis added).

That verse presents some very difficult concepts. "Begetting" normally speaks of a person's origin. Moreover, sons are generally subordinate to their fathers. I therefore found it difficult to see how an eternal Father-Son relationship could be compatible with perfect equality and eternality among the Persons of the Trinity. "Sonship," I concluded, bespeaks the place of voluntary submission to which Christ condescended at His incarnation (cf. Phil. 2:5-8; John 5:19).

My aim was to defend, not in any way to undermine, Christ's absolute deity and eternality. And I endeavored from the beginning to make that as clear as possible.

Nonetheless, when I first published my views on the subject (in my 1983 commentary on Hebrews), a few outspoken critics accused me of attacking the deity of Christ or questioning His eternality. In 1989 I responded to those charges in a plenary session of the annual convention of the Independent Fundamental Churches of America (the denomination that ordained me). Shortly after that session, to explain my views further, I wrote an article titled "The Sonship of Christ" (published in 1991 in booklet form).

In both instances I reemphasized my unqualified and unequivocal commitment to the biblical truth that Jesus is eternally God. The "incarnational sonship" view, while admittedly a minority opinion, is by no means rank heresy. The heart of my defense of the view consisted of statements that affirmed as clearly as possible my absolute commitment to the evangelical essentials of Christ's deity and eternality.

Still, controversy continued to swirl around my views on "incarnational sonship," prompting me to reexamine and rethink the pertinent biblical texts. Through that study I have gained a new appreciation for the significance and the complexity of this issue. More important, my views on the matter have changed. Here are two major reasons for my change of opinion:

1. I am now convinced that the title "Son of God" when applied to Christ in Scripture always speaks of His essential deity and absolute equality with God, not His voluntary subordination. The Jewish leaders of Jesus' time understood this perfectly. John 5:18 says they sought the death penalty against Jesus, charging Him with blasphemy "because he not only had broken the sabbath, but said also that God was his Father, making himself equal with God."

In that culture, a dignitary's adult son was deemed equal in stature and privilege with his father. The same deference demanded by a king was afforded to his adult son. The son was, after all, of the very same essence as his father, heir to all the father's rights and privileges—and therefore equal in every significant regard. So when Jesus was called "Son of God," it was understood categorically by all as a title of deity, making Him equal with God and (more significantly) of the same essence as the Father. That is precisely why the Jewish leaders regarded the title "Son of God" as high blasphemy.

If Jesus' sonship signifies His deity and utter equality with the Father, it cannot be a title that pertains only to His incarnation. In fact, the main gist of what is meant by "sonship" (and certainly this would include Jesus' divine essence) must pertain to the eternal attributes of Christ, not merely the humanity He assumed.

2. It is now my conviction that the begetting spoken of in Psalm 2 and Hebrews 1 is not an event that takes place in time. Even though at first glance Scripture seems to employ terminology with temporal overtones ("this day have I begotten thee"), the context of Psalm 2:7 seems clearly to be a reference to the eternal decree of God. It is reasonable to conclude that the begetting spoken of there is also something that pertains to eternity rather than a point in time. The temporal language should therefore be understood as figurative, not literal.

Most theologians recognize this, and when dealing with the sonship of Christ, they employ the term "eternal generation." I'm not fond of the expression. In Spurgeon's words, it is "a term that does not convey to us any great meaning; it simply covers up our ignorance." And yet the concept itself, I am now convinced, is biblical. Scripture refers to Christ as "the only begotten of the Father" (John 1:14; cf. v. 18; 3:16, 18; Heb. 11:17). The Greek word translated "only begotten" is monogenes. The thrust of its meaning has to do with Christ's utter uniqueness. Literally, it may be rendered "one of a kind"—and yet it also clearly signifies that He is of the very same essence as the Father. This, I believe, is the very heart of what is meant by the expression "only begotten."

To say that Christ is "begotten" is itself a difficult concept. Within the realm of creation, the term "begotten" speaks of the origin of one's offspring. The begetting of a son denotes his conception—the point at which he comes into being. Some thus assume that "only begotten" refers to the conception of the human Jesus in the womb of the virgin Mary. Yet Matthew 1:20 attributes the conception of the incarnate Christ to the Holy Spirit, not to God the Father. The begetting referred to in Psalm 2 and John 1:14 clearly seems to be something more than the conception of Christ's humanity in Mary's womb.

And indeed, there is another, more vital, significance to the idea of "begetting" than merely the origin of one's offspring. In the design of God, each creature begets offspring "after his kind" (Gen. 1:11-12; 21-25). The offspring bear the exact likeness of the parent. The fact that a son is generated by the father guarantees that the son shares the same essence as the father.

I believe this is the sense Scripture aims to convey when it speaks of the begetting of Christ by the Father. Christ is not a created being (John 1:1-3). He had no beginning but is as timeless as God Himself. Therefore, the "begetting" mentioned in Psalm 2 and its cross-references has nothing to do with His origin.

But it has everything to do with the fact that He is of the same essence as the Father. Expressions like "eternal generation," "only begotten Son," and others pertaining to the filiation of Christ must all be understood in this sense: Scripture employs them to underscore the absolute oneness of essence between Father and Son. In other words, such expressions aren't intended to evoke the idea of procreation; they are meant to convey the truth about the essential oneness shared by the Members of the Trinity.

My previous view was that Scripture employed Father-Son terminology anthropomorphically—accommodating unfathomable heavenly truths to our finite minds by casting them in human terms. Now I am inclined to think that the opposite is true: Human father-son relationships are merely earthly pictures of an infinitely greater heavenly reality. The one true, archetypical Father-Son relationship exists eternally within the Trinity. All others are merely earthly replicas, imperfect because they are bound up in our finiteness, yet illustrating a vital eternal reality.

If Christ's sonship is all about His deity, someone will wonder why this applies to the Second Member of the Trinity alone, and not to the Third. After all, we don't refer to the Holy Spirit as God's Son, do we? Yet isn't He also of the same essence as the Father?

Of course He is. The full, undiluted, undivided essence of God belongs alike to Father, Son, and Holy Spirit. God is but one essence; yet He exists in three Persons. The three Persons are co-equal, but they are still distinct Persons. And the chief characteristics that distinguish between the Persons are wrapped up in the properties suggested by the names Father, Son, and Holy Spirit. Theologians have labeled these properties paternity, filiation, and spiration. That such distinctions are vital to our understanding of the Trinity is clear from Scripture. How to explain them fully remains something of a mystery.

In fact, many aspects of these truths may remain forever inscrutable, but this basic understanding of the eternal relationships within the Trinity nonetheless represents the best consensus of Christian understanding over many centuries of Church history. I therefore affirm the doctrine of Christ's eternal sonship while acknowledging it as a mystery into which we should not expect to pry too deeply.

John MacArthur, “Reexamining the Eternal Sonship of Christ,” Journal for Biblical Manhood and Womanhood 6, no. 1 (2001): 21-23.