Mohamed Bangoura, who was born in Leeds, was stopped from boarding a flight home after visiting family friends in Brussels.
He was finally returned to the UK and reunited with his mother Hawa Keita after the Home Office issued him with an emergency travel document.
MEP Catherine Bearder and MP Sir Ed Davey wrote a joint letter to Home Secretary Sajid Javid last week calling for the boy's return.
They said he had been due to start school in Sheffield on Monday but his passport was rejected by Belgian authorities on August 27.
The Home Office said it sent a letter to Ms Keita, who is from Guinea, in March telling her Mohamed's passport had been revoked.
The joint letter sent by Ms Bearder and Sir Ed said Ms Keita "insists she never received a registered letter by courier or by email".
"Whatever error has been made on whoever's side, we must bring this child home now and reunite him with his worried mother," it added.
"His immigration status should be sorted when he is on home soil with his mother Hawa. All that matters is that we get a frightened six-year-old back to his mother."
A Home Office spokeswoman said Mohamed was taken out of the UK in July and was "unable to return as he did not hold a valid passport".
"Mohamed has now returned to the UK after an emergency travel document was issued allowing him to travel to the UK," she added.
The Home Office said Mohamed was only entitled to British citizenship through his mother or her husband, but neither was settled in the UK when he was born.