The president picked Lonergan's team, seeded ninth and making its first NCAA appearance since 2007, to lose to eighth-seed Memphis on Friday in Raleigh, N.C.
"You picked Memphis over your neighbors in Foggy Bottom? Come on man!" Lonergan tweeted at the president Wednesday night.
George Washington's campus sits a half-mile from the White House.
Lonergan went on to hope that First Lady Michelle Obama picked George Washington over Memphis.
The president also picked Washington's other NCAA entry, American, to lose. That's a bit different, as the school is a No. 15 seed facing long odds of beating second-seed Wisconsin.
Lonergan, a Maryland native who played college basketball at Washington's Division III Catholic University of America, later insisted he wasn't trying to inflame the city's often-fractious discourse.
"I was just joking around!" he wrote.