Billionaire Trump came into June with just $1.2m, while Clinton had $42.5m, according to the Federal Election Commission.
Including super PACs - which are organisations that support certain candidates - that have filed their fundraising reports, Trump's side had just short of $2m in cash while Clinton's side had $94m.
Looking at May, Trump was donated just $3.1m, while Clinton raised $28.3m, the Los Angeles Times reported.
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"We're starting the general election in strong financial shape thanks to the support of more than 1.3 million people and strategic investments that helped us conserve our resources," Clinton's campaign manager, Robby Mook, said in a statement.
It's the latest blow to Trump, who yesterday reportedly fired his top aide Corey Lewandowski, as the property magnate gears up for the general election.
The Associated Press reported that the Republican National Committee raised $13m in May, and had $20m on hand at the end of the month - just a third of the $60m it had banked at the same point in 2012.
Trump has also loaned his campaign more than $45m of his personal wealth.
However, it may not all be that concerning to the Republicans. Back in February it was reported that Jeb Bush - one time rival of Trump for the Republican nomination - had spent $130m on his campaign, with nothing to show for it.
Trump, meanwhile, had spent a minimal amount with free media exposure.