"Each time this administration elevates an outspoken opponent of LGBT equality, sometimes in particularly cruel ways like replacing the first openly gay Secretary of the Army with someone who called being transgender a 'disease', I picture all of the joyful, beaming couples that I've met across our country who are so excited to get married, start a family, and begin their lives together," Clinton said on Thursday night during a fundraiser for an LGBT (lesbian, gay, bisexual, transgender) community centre in New York.
The former presidential hopeful was referring to Trump's pick of Mark Green for the post, NBC News reported.
Author and columnist Arianna Huffington introduced Clinton, presenting her with the centre's "Trailblazer" award at the event.
Clinton called the administration's action insufficient following reports of the arrests and torture of suspected gay men in Chechnya.
"It's not just here in our country that we're seeing clouds gathering on the horizon," Clinton said.
"The US government, yes, this government, must demand an end to the persecution of gay men in Russia," NBC News quoted Clinton as saying.
Three others were honoured on Thursday night for their contributions to LGBT equality: fashion designer Marc Jacobs, ADP Chief Financial Officer Jan Siegmund, and New York City Commission on Human Rights Chair Carmelyn P. Malalis.
Clinton also addressed transgender youth, blasting the Trump administration for withdrawing a school guidance aimed at protecting trans kids.
"My heart broke for all the parents who are advocating so fiercely for their child's right to live, learn and go to school just like anybody else," she added.