Clinton made the appeal ahead of the 40th anniversary this month of New York's Stonewall Riots, often seen as the launch of the US gay rights movement, in which gays and lesbians fought back against police who raided their bars.
"The example set by those fighting for equal rights in the United States gives hope to men and women around the world who yearn for a better future for themselves and their loved ones," said Clinton, a former senator from New York.
While acknowledging that gays and lesbians still had a long path to equality in the United States, Clinton deplored that gays in some parts of the world live in constant fear of arrest or violence.
"The persecution of gays and lesbians is a violation of human rights and an affront to human decency, and it must end," she said.
"As secretary of state, I will advance a comprehensive human rights agenda that includes the elimination of violence and discrimination against people based on sexual orientation or gender identity."
Under President Barack Obama, the United States has switched gears from the previous George W. Bush administration by supporting a United Nations resolution calling for the global decriminalization of homosexuality.
Homosexuality is punishable by death in seven countries -- Iran, Mauritania, Nigeria, Saudi Arabia, Sudan, the United Arab Emirates and Yemen.
Last month, Congressman Howard Berman said Clinton had promised him that the State Department would offer equal benefits to partners of homosexual US diplomats stationed overseas.
Clinton in her statement saluted the service of "our lesbian, gay, bisexual and transgender employees in Washington and around the world."