Michael Adebowale stood before a packed courtroom where he nodded to confirm his name, date of birth, and address.
The charges - murder and possession of a firearms with intent to cause violence - were read out to him during the five-minute hearing.
He was wearing white trousers and a grey sweatshirt, and was handcuffed and flanked by two officers.
He will appear in court again on Monday for a bail hearing, and will face trial at the Old Bailey in due course.
Adebowale was charged following his release from hospital after authorisation from the Crown Prosecution Service (CPS).
He was injured when he and his alleged co-accomplice Michael Adebolajo, 28, were shot by officers at the scene of the attack in southeast London.
Adebolajo remains in hospital in a stable condition.
Drummer Rigby died of multiple stab wounds following an attack on May 22nd.