The substitute replaced Ander Herrera in the 85th minute as Ole Gunnar Solskjaer wanted to see out the clean sheet.
And when Bailly was waiting for the midfielder to leave the field, Phelan gave the former Villarreal man a shoulder rub to ensure he was ready for action.
The 24-year-old had his game face on and did not seem phased by the bizarre behaviour.
Fans did pick up on it though and were amused by what they were witnessing.
One tweeted: “Mike Phelan massaging Eric Bailly’s shoulders at the touchline as he waits to replace Ander Herrera should be in the #MUFC Museum.”
“Mike Phelan massaging Bailly’s shoulders before coming on has got to be my Golden Moment of the Year. Love it,” another said.
A third added: “Mike Phelan massaging Bailly’s shoulders before he came on is absolutely hilarious!”
The Manchester United cruised to victory in west London against relegation strugglers Fulham.
Paul Pogba gave them the lead when he smashed the ball past Sergio Rico at his near post.
The Frenchman now has 13 goals this season, his previous highest-scoring campaign saw him net 11.
Anthony Martial then got in on the act when he used his blistering pace to surge through the Fulham defence.
He then had the finish to match as the team celebrated in front of the travelling fans.
Juan Mata was brought down in the second half and Pogba made no mistake from the spot.
Solskjaer made six changes to his starting line up and the rotation paid off.
United are now on 51 points and one clear of Chelsea who travel to Manchester City on Sunday.
Premier League Player of the Month Marcus Rashford was one of the rested star.
He will now be fresh for the visit of Paris Saint-Germain when the Champions League returns in midweek.