The schoolboy, who moved to Sweden from Latvia last summer, had been playing for a youth team in Haninge, a small town just south of Stockholm.
But while he was away on holiday, his parents were informed that he was no longer allowed to play for the club, because his Swedish was not good enough.
"We find it hard to see that [boy's name deleted] can take part in the team if he does not know the language," read the text message sent to the family and first reported by Sveriges Radio.
The boy's mother told the broadcaster that her son had "started to cry" when he had learned of the news and said he did not want to return to Sweden after their break.
"I got sad, I understood that I would have to sit at home and do nothing instead of playing football," the young player added.
IFK Haninge issued an online apology on Thursday, noting that the coach who had sent the message had resigned and confirming that the boy was welcome to return to one of its youth teams.
"It has never been the case that someone is prevented from playing with us because he or she cannot speak Swedish," said the club's sports director Omar Moggi in the statement.
"We have many children in the club who can't speak Swedish," he added.
In a text message to The Local he said he was not available for further comment during the afternoon.
Meanwhile the club's president Niclas Lindberg also said sorry for the incident, describing the club as a "friendly society".
His online comment explained that the club's own constitution stated that potential members should be welcomed "regardless of their nationality, ethnic origin, religion, age, gender or sexual orientation or physical or mental condition".
News of the schoolboy being booted out of the club comes days after Sweden's Prime Minister Stefan Löfven suggested that sport could be a key way to integrate immigrants in the Nordic nation, which is processing record numbers of residency requests from both asylum seekers fleeing conflicts and people moving between EU member states.