The unnamed player experienced mild symptoms and is feeling fine.
The MLS season was suspended last month due to the coronavirus pandemic, which has led to more than 47,200 deaths worldwide.
"Philadelphia Union today announced that a Union player has tested positive for the novel coronavirus [COVID-19]," the team said in a statement.
"The Union medical staff has been working directly with Crozer-Keystone Health System medical officials to treat the player who experienced mild symptoms and is feeling well and in good spirits.
"The player is observing appropriate isolation protocols. No other cases or symptoms within Philadelphia Union soccer operations have been identified at this time.
"No Philadelphia Union players or technical staff have trained or been at the Power Training Complex facility or Subaru Park since Thursday, March 12.
"Based upon guidance from Crozer-Keystone Health System medical officials, infectious disease specialists and Major League Soccer health officials, this case does not present a risk to our fans, our most recent opponent, LAFC, or any of the other Union players, staff, or personnel and Union players and personnel do not need to be tested as the team is outside of the 14-day window where anyone with team related interactions with the player would have reported symptoms."
Philadelphia were winless through two games when the MLS season was stopped, collecting one point.