In a ruling published on Tuesday, the BAI compliance committee unanimously found the programme had treated the issue “fairly and was presented in an objective manner”.
The BAI considered three complaints about the broadcast, all of which claimed that the programme was imbalanced and harmful to transgender people.
The show, which aired in January, featured a pre-recorded interview with Father Ted writer and anti-transgender activist Graham Linehan.
Prior to broadcast, an online petition urging the national broadcaster not to run the piece had gained over 5,000 signatures.
The 51-year-old – who has been active in his anti-transgender activism – has been given a verbal warning by police after a complaint by a transgender activist following a dispute on Twitter about gender identity.
The Committee relayed in their acknowledgement "that some comments made by contributors were controversial, however, at the outset of the programme the presenter provided context for the topic and outlined the nature of the discussion."
In response RTÉ said it had aimed to examine two issues - the implications of Ireland having passed the Gender Recognition Act 2015 and proposals to allow minors to change gender.
It stressed the important role commentators play in public debate and said it would be wrong to limit contributors to people with personal experience or expertise.