Michael Adebowale, 22, was quiet and uttered one word -- "yes" -- to confirm his name and address, and nodded to acknowledge the district judge's comments at the end of the 5-minute hearing at Westminster Magistrate's Court, The Daily Telegraph reported.
Security was tight at the courthouse and Adebowale was restrained in handcuffs.
Rigby was killed near Woolwich barracks last week. An examination found his death was caused by "multiple incised wounds." An inquest is scheduled for Friday.
Adebowale's right hand was bandaged when he and another suspect, Michael Adebolajo, were shot by police. The Telegraph said Adebowale is believed to have lost several fingers during the incident in southeast London and was shot by police from an armed response vehicle.
Adebowale, among eight people arrested in the slaying, was asked if he understood he was charged with Rigby's death and of possessing a 9.4mm KNIL Model 91 revolver "to cause persons to believe that unlawful violence would be used."
Prosecutor Bethan David told the court he understood a hearing was set for June 28.
A hearing is scheduled for Monday to bring the case under the terrorism protocol that governs how terrorism prosecutions are heard in court, David said.
Judge Howard Riddle noted the charges were read to Adebowale and pleas "will be sent to the Central Criminal Court sitting at the Old Bailey."
"This court cannot grant bail," Riddle said.
He said the plea and case management hearing would be June 28.
Adebolajo remains in hospital.