The two-time Olympian will compete at U.S. indoors this weekend.
Ben True wins a stacked men's 5,000m; Molly Huddle runs second-fastest 10,000m ever for an American woman.
His Oregon Project teammate, Matthew Centrowitz, has withdrawn from the race.
The 17-year-old Cain took nearly a second off the previous mark.
The American runner shared his life story last week.
The Americans bring a strong field to this year's race in the heart of Manhattan.
The 17-year-old finished second in the women's 1,500m final at the U.S. Championships.
Most of the pre-meet contenders advanced through the preliminary rounds.
The Sudan native came to the U.S. in 2001 as one of the "Lost Boys."
All seven starters set an indoor personal best.