Saint Alphonsus Regional Medical Center spokeswoman Jennifer Krajnik said Friday the man died overnight at the hospital.
United spokeswoman Christen David said early Friday morning in an email that the man was the captain on the flight.
The airline did not give his name, citing privacy reasons.
A Boise airport spokeswoman said Thursday that the man suffered an apparent heart attack.
Passengers told Seattle TV station KOMO the crew remained calm.
United Flight 1603 with 161 passengers was flying from Houston to Seattle when the medical emergency forced it to make the landing about 8 p.m. in Boise.
David says another pilot flew the original plane and passengers to Sea-Tac Airport.