Clinton says the justices should overturn the Defense of Marriage Act he signed in 1996 that bars the federal government from recognizing same-sex marriages. He said the law is inconsistent with "equality and justice" under the law.
"I have come to believe that DOMA is contrary to those principles and, in fact, incompatible with our Constitution," Clinton wrote in an op-ed article in The Washington Post newspaper.
Clinton's reversal follows a brief filed March 1 by the Obama administration that urges the Supreme Court to reinstate same-sex marriage in California and calls for broad constitutional protections that ultimately could allow such unions nationwide.
Clinton's support in a newspaper article is more symbolic and not formally part of what the court is considering.
The court will hear arguments on the California case and DOMA later this month.
The law defines marriage as being between a man and a woman. Clinton wrote that it was "a very different time" in 1996 and that Americans since then have shifted their thinking.
Today, same-sex couples who are legally married in nine states and the District of Columbia are denied the benefits of more than a thousand federal statutes and programs available to married heterosexual couples, Clinton said.
"These couples cannot file their taxes jointly, take unpaid leave to care for a sick or injured spouse or receive equal family health and pension benefits as federal civilian employees," Clinton wrote. "Yet they pay taxes, contribute to their communities and, like all couples, aspire to live in committed, loving relationships, recognized and respected by our laws."
"Reading those words today, I know now that, even worse than providing an excuse for discrimination, the law is itself discriminatory," the former president wrote. "It should be overturned."