The Scotland captain will see a specialist this week and could be out for at least a month if he needs an operation.
Any absence would be another blow for the 30-year-old who only returned to first team action at the turn of the year after a lengthy lay-off due to a bowel problem.
He is desperate to get a full close season under his belt after making a full recovery from ulcerative colitis which had threatened to end his career and troubled him for more than two years.
Fletcher made 12 appearances after his return in December, including the 1-1 final day draw at Southampton. He started and finished the game and was only made aware of the broken toe after the match.
Manchester United medical staff and doctors decided the injury did not need surgery initially but the toe has been slow to heal and the club and player want a fresh opinion to decide if an operation is necessary.