The research - published as correspondence in The Lancet - found that across more than 10,000 Wellcome Trust grants allocated between 2001 and 2008, women received an average of ?44,735 less per grant than men.
The results were a surprise, said the study's lead author, Gillinder Bedi, assistant professor of clinical psychology at Columbia University and a research scientist at the New York State Psychiatric Institute.
"To put it in context, the average grant for men was around ?300,000 and for women around ?250,000, so it's a significant proportion of that," she said.
To try to correct for the under-representation of women at top levels - a possible cause of the disparity - the research team made allowances for whether applicants were at pre-doctoral, postdoctoral or professorial level.
Given that UK funders rarely award less than the amount sought, the team - which also included Nicholas Van Dam of the Mount Sinai School of Medicine in New York and Marcus Munafo, professor of biological psychology at the University of Bristol - concluded that the most likely explanation was that women were seeking smaller sums.
But Athene Donald, professor of experimental physics and chairwoman of the Gender Equality Group at the University of Cambridge, said that although other research had shown that women were likely to ask for less than men in pay negotiations, there was not enough evidence to infer a similar effect in grants.
"They tried to split it by grade, but that doesn't alter the fact that the men might be more senior within professorial rank or [that there could be] other explanations, for example that women may be working in areas that are cheaper," she said.
A spokesman for the Wellcome Trust agreed that the study's attempt to take into account differences in grades was too crude to draw any conclusions. However, he added that the trust was aware that fewer women in senior positions applied for grants and that this was something it was taking steps to address.