Muamba, 24, almost died after suffering cardiac arrest in an FA Cup tie against Tottenham Hotspur at White Hart Lane in March when he collapsed on the pitch and needed life-saving treatment.
His heart stopped for 78 minutes but the former midfielder made a remarkable recovery, spending four weeks in an east London hospital.
Muamba travelled to Belgium last week to seek medical advice from a leading cardiologist but his hopes of resuming a playing career were dashed.
"The news I received was obviously not what I had hoped it would be and it means I am now announcing my retirement from professional football," Muamba said on the Bolton website.
"Since suffering my heart attack and being discharged from hospital, I have remained utterly positive in the belief I could one day resume my playing career and play for Bolton Wanderers once again.
"Football has been my life since I was a teenage boy and it has given me so many opportunities."
Muamba moved to the London borough of Waltham Forest from the Democratic Republic of Congo when he was 11 and represented England at every youth level from under-16 to under-21.
He also played for Arsenal, where former team-mate Robin van Persie said he always had a "smile on his face" and Birmingham City.
"Football's lost a good man. It'll be a blow to the kid," said former Birmingham boss Alex McLeish.
Bolton manager Owen Coyle also spoke of his admiration for Muamba.
"Everyone has seen what a fighter and strong person he is in mind and body.
"We know that he will go on to achieve great things and within all this disappointment, the most important thing is that he is here, alive, today," said Coyle.
Muamba jogged with the Olympic torch when the relay reached the capital's suburbs last month.
"I pay tribute once again to the members of the medical team who never gave up on me," added Muamba.
