Johan Adam Heyns was born on the farm Bloemkraal at Tweeling in the Orange Free State, South Africa.
His father, Flip Heyns, wanted to become a missionary, but could not afford to do so and became a farmer instead. His mother, Maria Beukes, was exiled to Saint Helena during the Second Boer War. Her marriage to Flip Heyns was her second. Since her first marriage did not produce any children, Maria promised God that if He would bless her with a son, she would raise him for His service. Although she did not tell Heyns about this promise until years after he had already been ordained as minister, Heyns would later admit that his mother had played a significant role in his eventual decision to become a cleric.
Being an Afrikaner was important to Heyns since his schooldays. His interests in politics started early, and he became a leader of a youth group in the Ossewabrandwag while still in primary school. (During breaks he would hold meetings and make speeches - an activity which was stopped by the school principal). Despite his father being the leader of the local branch of the National Party and Heyns’ early affinity for politics, he would never formally join the ruling party. Although he maintained a strong pro-national stance, his views were tempered through his ability to maintain a unique critical perspective – an asset which would later become a hallmark of his work.
During his high school years the family moved to Potchefstroom and operated a boarding house. His love for the Bible and his faith in God was noted by several theology students who were lodging at the Heyns’ residence. At school Heyns was an average student, and showed little interest in the subjects at hand. He did however display a flair for debate and independent thinking on complex topics - after one such discussion (regarding Darwin's evolutionary theory) one theology student voiced his concern to Heyns’ parents that the young man might be losing his mind.
Johan Heyns completed his undergraduate studies at the Potchefstroom University for Christian Higher Education where he formed a lifelong friendship with Hendrik G. Stoker, the South African Calvinistic thinker and a central advocate of the Philosophy of the Cosmonomic Idea. Stoker’s reasoning had a marked influence on the rest of his academic career.
Heyns completed his training as a minister at the University of Pretoria, and decided to continue his theological studies at the Free University in Amsterdam. In 1953 he obtained a Ph.D. under the supervision of G. C. Berkouwer with a thesis titled Die Grondstruktuur van die Modalistiese Triniteitsbeskouing (The Basis of the Modalistic Trinity View).
In 1961 he obtained a second Ph.D. (in philosophy) under the supervision of Stoker. His thesis was titled Die Teologiese Antropologie van Karl Barth vanuit Wysgerig-Antropologiese Oriëntering (The Theological Anthropology of Karl Barth from a Philosophical-Anthropological Orientation).
In 1954, after completion of his theological studies in Amsterdam, Heyns became an ordained minister and served at the Ysterplaat congregation of the NGK. Towards the end of 1960 he transferred to Rondebosch where he counted several Afrikaner politicians amongst his flock (including Hendrik Verwoerd, John Vorster, and PW Botha).
Heyns' academic career started in 1966 when he was appointed as lecturer in dogmatic subjects at the University of Stellenbosch. In 1971 he succeeded A.B. Du Preez as professor at the University of Pretoria where he stayed until his retirement at the end of 1993.
During the more than 20 years that Heyns served the NGK as a professor, he exerted an enormous influence on the church. He was distinguished by a large number of publications and he filled many public positions in the church, causing him to be regarded as one of the best known theologians in the NGK.
Upon his retirement, a special edition of the NGK journal at the University of Pretoria (Skrif en Kerk) was dedicated to Heyns' influential theological work. In it friends and theological colleagues dialogued with Heyns' theological work from different angles. Contributions were made by such theologians as Conrad Wethmar, Willie Jonker and Jurie le Roux. The latter's contribution created a rather significant and controversial theological discussion, the effects of which is more and more evident in the "liberal" course the NGK has taken since Heyns' death. Jurie le Roux, NGK Old Testament biblical scholar from Pretoria at the time (who is, strangely enough politically conservative but theologically more "liberal"), accused Heyns of not engaging with the "unchallengeable results of historical criticism" ("onaanvegbare resultate" van die historiese kritiek). Had he done so, he would presumably have agreed with Le Roux that 1) It is impossible to speak of the unity of Scripture's message; 2) The settled think patterns ("gevestigde denkpatrone") of Christianity should be left behind in full; 3) The church can no longer speak about its message with authority; 4)The "light" of Revelation does not fall on the whole cosmos any longer ). Heyns responded with grace, but also expressed his serious concern about Le Roux's deductions from historical criticism. Heyns wrote: "if the acceptance of the unchallengeable results of historical criticism leads and forces the theologian to such interpretations, then to my mind it represents a dangerous road to follow - for the systematic theologian and the biblical scholar".  163. Heyns' words were prophetic, in light of i.e. Le Roux's extraordinary supportive review article of Jesus Seminar scholar, Andries Van Aarde's controversial historical Jesus book: Fatherless in Galilee published in 2003
In the 1980s and the early 1990s Heyns became a central figure in the struggle to change the NGK’s stance on Apartheid, leading to the church’s eventual rejection of that policy. In 1982 Heyns publicly rejected the notion that Apartheid was the will of God, and caused a furor at that year’s synod by openly supporting multiracial marriages. For a year he stayed out of favor with the church hierarchy, but reemerged in 1986 to become moderator - the highest position in the church. He immediately tried to persuade the church that there was no biblical foundation for Apartheid.
Following the NGK Synod of 1986 (at which Heyns presided), tens of thousands of church members and congregations broke away to form the Afrikaans Protestant Church. In September 1989, at a time when the government indiscriminately crushed all protest marches, mediation by NGK leadership under Heyns convinced the government to allow peaceful protests. This heralded the first swing away from the armed struggle to a strategy of non-violent confrontation.
In 1990, speaking for the NGK, Heyns declared Apartheid a sin. His theological contributions had a large impact on changing the thinking of the Afrikaner government.
On Saturday evening, 5 November 1994, Heyns was playing cards with his wife and three grandchildren (then aged 2, 8 and 11) at his home in Pretoria. He died instantly when an unidentified attacker using a .303 caliber rifle delivered a single gunshot through a window. The bullet entered at the back of his neck and left near his eye, leaving a wound as big as a man's fist.
Although the police would not speculate on a motive, many were convinced that Heyns was killed by white extremists. Shortly after his assassination a secretary of Die Burger, an Afrikaans newspaper, received threats that three Afrikaans-speaking cabinet members would be next. The caller told the secretary that he had already lost everything as a result of affirmative action: "We belong… I belong to no organization. And this will not be the last one." Subsequent threats followed, indicating that Mandela was also a target.His Biblical view against Apartheid that led to the schism with and founding of the Afrikaanse Protestantse Kerk and the declaration of Apartheid as a sin was experienced by some as an act of treason against the political and ethical values and aspirations of the Afrikaner.
Heyns' assassin left very few clues, and no arrests have been made. In the book "The Tall Assassin: the darkest political murders of the old South Africa" it is claimed that he was killed because he was a double agent.