The top 125 players on a season-long points list after Sunday’s Wyndham Championship qualify for the first of four playoff events.
A few players usually skip the Northern Trust after a busy summer stretch, preferring to rest up for the remainder of the playoffs and, in even-numbered years, the Ryder Cup.
Northern Irishman McIlroy suggested after a disappointing equal 50th finish at the PGA Championship last Sunday that he might not enter the Northern Trust, to be held this year at Ridgewood Country Club.
Fowler has a partially torn abdominal muscle and has decided to rest as a precaution.
Fowler hopes to be back in time for the Ryder Cup in six weeks. He has qualified for the American team to play Europe in Paris.
The only other currently eligible player planning to sit out next week is 96th-ranked American Patrick Rodgers.
Former world number one Tiger Woods has entered after qualifying for the playoffs for the first time since 2013.