An audio exhibit revealed how people's explanation of how the Causeway was formed developed as scientific understanding improved.
Young earth creationists believe the Causeway was formed 6,000 years ago. The vast majority of scientists say it was formed 60m years ago.
The trust says it has always supported the "scientific view" of its formation.
The Causeway is a Unesco World Heritage Site and features more than 40,000 interlocking basalt columns.
The £18.5m centre was opened on 3 July.
The National Trust decided to carry out a review of the exhibit after the creationist element provoked what it termed a "wide and mixed response".
In July, an online campaign to remove it began.
A new piece of audio, approximately 20 seconds long, now replaces the previous recording.
Graham Thompson, project director for the Giant's Causeway, said the change would clear up "any misunderstanding there may have been".
"The National Trust is content that this review is complete."He said: "The National Trust only endorses the scientific explanation of the origins of the stones, yet recognises that others have alternative beliefs.