Speaking at the Sydney WorldPride Human Rights Conference about homophobia in sport, he blamed the media for sensationalist speculation about his sexuality.
"I was directly asked by a journalist at 16 if I was gay," he said on Wednesday.
"That headline was ready to print on the basis of my answer and this was leading into the Olympics - so at the time I only thought of being gay as a negative."
Reporters would not ask a minor such a question today, but Thorpe pointed to various football codes for entrenching casual and blatant homophobia, singling out Manly Sea Eagles rugby league players for not playing in a Pride Round last year.
"The NRL has basically copped out and is looking at introducing a respect round," he said on Wednesday.
Thorpe questioned why athletes weren't "willing to actually wear a few colours on their shirt that means so much to so many people".
He appealed to athletes to show empathy and "understand what it's like for a young gay person to grow up and to face disadvantage and discrimination".
The three-day conference is part of Sydney WorldPride, with 60 local and international presenters, including LGBTQI campaigners and activists, policy and law makers, politicians, researchers and academics.
Health Minister Mark Butler announced a 10-year national health plan focused on LGBTQI communities, promising $26 million for medical research.
The plan is designed to address health disparities and make improvements across the health system for diverse sexual communities.
"There is so much work we need to do to close the gap in health and particularly mental health outcomes for LGBTIQA+ Australians," he told reporters at the conference.
Advocates such as Equality Australia CEO Anna Brown hailed the plan as "life-saving".
"This funding package for new research – the largest ever for LGBTIQA+ health – is incredibly welcome news for the many people in our communities who feel their needs have not been met by the health system," she said.
Joe Ball, head of mental health service Switchboard in Victoria, described the announcement as "a healing moment" for sexually diverse communities.
"We have the poorest mental health of any single cohort in Australia and for the transgender we have the highest rates of suicide," he said.
"This is a crisis but ... this is not because of who we are... but how we have been treated across our lifetime".
Speaking via video message, Foreign Minister Penny Wong announced the country's first dedicated fund to support LGBTIQ human rights groups in addressing social stigma and legal discrimination.
The Inclusion and Equality Fund will be granted $3.5 million this year.
Earlier in the day, Sydney WorldPride CEO Kate Wickett opened the conference urging attendees of the festival to "party with purpose".
"We celebrate united as a community that comes together and Mardi Gras is a visible display of that unification and celebration but the human rights conference is the embodiment of that purpose," she told AAP on Wednesday.
"We've still got a lot of work to do to achieve equality."
The UN's Independent Expert on Sexual Orientation and Gender Identity Victor Madrigal-Borloz said measures to ban gay conversion therapy in NSW, such as the bill by independent MP Alex Greenwich, were crucial.
The MP said earlier this month he would introduce the bill regardless of which party was elected on March 25.
Mr Madrigal-Borloz warned the fight towards repealing laws that criminalise sexual orientation and gender identity was far from over, with 67 countries still having them on the books.
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