"I encourage players, sports people to declare their sexual orientation without fear," she told reporters in Geneva.
"That's the only way they will find the right to sexual orientation accepted. They are role models, it's important to send this message to their fans as well," Pillay said, adding that it was "a shame, in this day and age", that people "had to hide who they really are".
She was speaking after addressing a meeting on equality in sports on the sidelines of the U.N. Human Rights Council, where she also spoke out against discrimination on the grounds of race or disability.
"There's an increasing realisation that combatting discrimination requires more than superficial measures that do not change attitudes or address the root causes of inequality," she told the meeting.
Pillay also warned governments that bid for major sporting competitions that they needed to give far more thought to how their bid would affect human rights.
This year's World Cup hosts Brazil and the 2022 hosts Qatar have both drawn criticism - Brazil for the $11 billion cost in a country where schools and hospitals are poor, and Qatar for suspicions of corruption and the welfare of migrant labourers.
"They risk becoming hubs of human rights violations, including misuse of public funds, child labour, forced evictions, and demolition and the sexual exploitation of human beings including children in the surge of tourism," Pillay said, without naming any particular city.
"Sporting events should celebrate the joy of human potential, not generate pain and abuse," she said.
(Reporting by Tom Miles; editing by Justin Palmer)
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