The duo were paired together but had vastly different fortunes in the first round at Royal County Down on Thursday.
Northern Ireland's world number one McIlroy shot a nine-over-par 80 and faces missing another cut, having failed to progress at the BMW PGA Championship at Wentworth last week.
American Fowler, meanwhile, returning to the country for the first time since 2007, fired four birdies in a solid level-par 71 to sit four strokes behind clubhouse leader Padraig Harrington of Ireland and nine ahead of McIlroy.
Fowler has happy memories of the course, having previously visited Royal County Down as a member of the victorious USA Walker Cup team eight years ago.
That week Fowler and team mate Billy Horschel beat McIlroy -- then amateur world number one -- and partner Jonathan Caldwell in the foursomes as the USA won the event by one shot.
Fowler and McIlroy, two of the leading lights and most consistent performers on the European Tour, have since become friends and the American sympathised with McIlroy's struggles.
"It was tough to see and you don't want to see someone struggle, and it was not the start he was looking for this week," the world number nine told reporters.
"But that's golf. We've all been through it, and I'm sure we'll go out and have some fun, and hopefully feed off each other tomorrow."
It was McIlroy's highest regular European Tour score since an eight-over 80 at the 2010 Open Championship at St Andrews.
"Nothing went right and I was trying hard to birdie the last to try and break 80, but it just didn't quite happen," a despondent McIlroy told reporters.
(Editing by Tom Hayward)
