The Stanford University endowment posted a 0.4 percent loss on its investments for fiscal 2016, underperforming some large rivals but doing better than Harvard University's 2.0 percent loss.
Last week, Yale University said it had a 3.4 percent gain for the year ended June 30.
The median return for foundations and endowments tracked by the Wilshire Trust Universe Comparison Service was negative 0.3 percent.
Harvard is the the largest university endowment, with $35.7 billion in assets. Harvard president Drew Faust said the "disappointing" investment return would "constrain our budgets,'' according to the Harvard Crimson.
Harvard Management Co. is seeking a new chief executive after the departure this summer of Stephen Blyth after a short, year-and-a-half stint. The endowment manager is under pressure to boost performance; Blyth had said it needed to produce at least a 5 percent return annually to meet its obligations to Harvard's annual operating budget.
Despite last year's loss, Stanford's endowment increased in value by 0.8 percent to $22.4 billion, the school said, thanks to fundraising and gifts.