The latest research, led by Erasmus University, found women are less intelligent than men by approximately 3.75 IQ points and do significantly worse in tests of spatial ability.
Lead author Dr Dimitri van der Linden said: "We found that men's brains are larger than women's and our analysis suggests this is the reason for lower average general intelligence across a range of tests.
"We are aware of previous research suggesting women's brains are better organised or process information more efficiently but we did not look at this in our study."
The study supports the controversial and now broadly forgotten claims of Charles Darwin in the 19th century that men's brains were larger than those of women.
Darwin, who once reasoned that a wife was "better than a dog, anyhow", said women's brains were halfway between that of a child and a man.
Today's scientists have MRI scans to calculate brain volume and past studies have agreed that men's brains are larger. The latest study took scans and cognitive tests from 896 people aged 22 to 37 as part of the Human Connectome Project.
Published in the journal Intelligence, the research says men had higher scores on most measures of intelligence, including spatial awareness.
Women did better in memory tests, including recalling a sequence of 18 pictures, but analysis found this made no difference to their general intelligence.
Brain size in the sexes is hotly debated in the scientific community.
Dr Joseph Devlin, head of experimental psychology at University College London, said: "This is a well-researched study but the evidence is not strong enough to prove that larger male brains are more intelligent than smaller female brains, which makes it a leap of faith, using a measure of general intelligence which has little basis.
"Men and women's brains are different and we know spatial navigation is slightly better in men than women, while women tend to have a better vocabulary. But we should be sceptical of claims that men are smarter than women, especially when there is little to no evidence for that and lots of evidence to the contrary."
University of California research found women's brains are smaller but could perform more quickly because of better connections between brain cells.