Mum Fehnez Khan, of Solihull, West Midlands, claims her nine-year-old son was substituted by his team's manager because he is Asian during a match.
Now police and Birmingham FA are investigating the claims, which have been strenuously denied by the club, Knowle Juniors.
Police were called in by the Khans following a touchline verbal exchange between the boy's older brother Mohysn, 22, and other parents.
Fehnez, who has asked for her little boy's name to be withheld, said: "My son is devastated and upset. He was substituted more than any other child.
"I want an apology to my son and a refund of the £160 subs I paid because the club did not benefit him."
Knowle Juniors, who are in the Warwickshire League, which runs 22 teams, denies the race claims.
A spokesman said "We are very upset by these allegations. We have taken statements from nine parents, including those of an Asian player.
"They have all said this is a football, not racial, issue.
"The manager has had so much support from parents. Mrs Khan wants the manager and assistant removed. There is no way that is going to happen."
The club said Mrs Khan's son was not the only player to be subbed.
"There are two other children who have got less game time," said the spokesman.
A Birmingham County FA official said "We have received a complaint and are currently investigating it."
A spokesman for West Midlands Police said "We are aware of the situation and hope to resolve this locally."