Lacey Police Lt. Phil Comstock said the boy, whose name has not been released, died Sunday night at Mary Bridge Children's Hospital in Tacoma.
The boy's father found him in the pool at the Diamond Head Apartments about 4 p.m. Saturday.
Officials said the father had fallen asleep and when he woke up he noticed the child had left the apartment.
He searched the apartment complex grounds and found his son unconscious in the pool and began performing CPR until medics arrived.
The boy was taken to St. Peter's Hospital in Olympia and then airlifted to Mary Bridge Children's Hospital.