The Illinois senator's presidential campaign raised $32.5m (£16.2m) in the period from April to June, a record for a Democratic candidate, his team said.
Mr Obama has now collected a total of $55.7m (£27.9m) in funding.
But Mrs Clinton, whose team said she raised around $27m (£13.5m) in the same quarter, still leads in opinion polls.
Former Senator John Edwards said his campaign had garnered a second-quarter total of just over $9m (£4.5m) from some 100,000 donors.
Other Democratic candidates Bill Richardson and Christopher Dodd reported raising $7m (£3.5m) and $3.25m (£1.6m) respectively.
Republican candidates have not yet announced their funding totals for the second quarter but are expected to do so well in advance of the 15 July deadline for submitting reports to the Federal Election Commission.
Mr Obama said he received at least 154,000 contributions in the last accounting period, bringing the total number of donors to 258,000 in the first half of the year.
Mr Obama said his was the "largest grassroots campaign" for this stage of a presidential race.
"We now have hundreds of thousands of Americans who are ready to demand health care for all, energy independence and an end to the war in Iraq," Mr Obama said.
"That's the kind of movement that can change the special interest-driven politics in Washington and transform our country, and it's just the beginning."
According to campaign aides, $31m of Mr Obama's total funds are earmarked for use in party primaries.
In the first quarter of the year, Mr Obama raised at least $25m (£12.6m) and Mrs Clinton raised $26m (£13).
However Mrs Clinton has an extra $10m (£5m ) on top of these donations, left over from her earlier Senate campaign.
On the Republican side, former Massachusetts Governor Mitt Romney indicated on Friday that his second quarter funds fell short of the $21m (£10.5m) raised in the first quarter.
Rudolph Giuliani, who raised nearly $15m (£7.5m) in the first quarter, is expected to announce his figures on Monday or Tuesday.
Senator John McCain is hoping to come in third in the Republican fund-raising stakes, correspondents say.
He announced an overhaul of his fundraising operation in April after declaring a disappointing $12.5m (£6.2m) for the first quarter of 2007.Money pledged for the presidential election in November 2008 - should a contender become their party's nominee - cannot be spent on campaigning for the primary.