Karolinska Institute was the highest ranking Swedish university with a rank of 44th, dropping eight places from last year's results.
Both Stockholm and Uppsala University, meanwhile, jumped inside the top 100 at equal 98th. Last year, they were ranked at 103rd and 111th respectively.
Lund University (119th) and the Royal Institute of Technology (126th) were not far behind.
Phil Baty, the editor of the study, pointed out that it was a mixed bag of results for Sweden's higher education.
"Although its top ranked university has slipped, this has been a strong year for Sweden in the rankings, as it now has three top-100 universities compared to just one last year," he said in a statement.
"The data shows that Sweden clearly has a strong and globally competitive system, with a total of ten institutions making the top 400, but there is evidence of greater polarisation between the best and the rest, as the lower-ranked institutions have slipped closer to the bottom of the table and are at risk of falling out."
Another five Swedish universities featured inside the top 400.
The California Institute of Technology held on to the world number one spot for the fourth consecutive year, ahead of Harvard University in second and the University of Oxford in third.