"If somebody doesn't have equal rights, then none of us are free," activist Jason Yanowitz, 37, told the Associated Press.
Protester Joel Freedman said it was "absolutely ridiculous" that gay men and women "work so hard to support this country" but do not have full equality.
"It's just absurd. It's absolutely absurd. It's enough," he said.
The main speaker at the rally, Julian Bond - who chairs the prominent rights group the National Association for the Advancement of Colored People (NAACP) - compared gay rights to the civil rights movement.
"Black people of all people should not oppose equality and that is what marriage is all about," he said.
"We have a lot of real and serious problems in this country, and same-sex marriage is not one of them. Good things don't come to those who wait, but they come to those who agitate."
Since coming into office, Mr Obama has taken steps towards addressing gay rights issues, including extending some benefits to the spouses of gay federal employees, the BBC's Imtiaz Tyab in Washington reports.
Married gay and lesbian couples are also allowed by the state department to obtain passports with their married names.
But the president has been criticised for not delivering on his promise to repeal the Defense of Marriage Act, which limits how local and federal bodies can recognise gay partnerships and determine benefits.
Polls consistently show there are far more opponents of gay marriage than there are supporters, says our correspondent.
In his speech on Saturday, Mr Obama said: "I appreciate that many of you don't believe progress has come fast enough. Do not doubt the direction we are heading and the destination we will reach."
He was speaking to America's largest gay group - the Human Rights Campaign - in Washington.
On the military issue he said the US could not afford to lose those people who had much needed skills for fighting.
"We should not be punishing patriotic Americans who have stepped forward to serve the country," Mr Obama said.
"We should be celebrating their willingness to step forward and show such courage."
The chair of the Senate Armed Services Committee, Democrat Senator Carl Levin, said he supported the repeal but that it had to be done "in the right way".
"We can do it successfully, but it ought to be done with thoughtfulness and care, and with buy-in from the military," he told NBC.
Mr Obama did not give a timetable for repeal of the policy, passed by Congress in 1993, under which thousands of service members have been discharged.
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