The 29-year-old singer was recognised for her support of the LGBT community and for speaking out against bullying and harassment of lesbian, gay, bisexual and transgender youth, reported E! online.
Accepting the award, Kesha referenced her recent struggles which have seen her embroiled in a contract dispute with Sony.
Last month a judge denied her request to be freed from her contract with Sony and producer Dr Luke, whom she has accused of physically, mentally and sexually abusing her.
Dr Luke has always denied the allegations.
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During her speech the singer appeared visibly choked up and had to take a moment to compose herself.
The singer went on to say that growing up, she was a "misfit" and was drawn to others in the LGBT community.
Even after finding success Kesha said she still feels like an outsider and had trouble dealing with criticism she received for just being herself.