James Burder and Adam King were accused of killing the popular 16-year-old through “gross negligence”.
Megan’s body was found on the back seat of a car which collided with a motorcycle last weekend.
The defendants, who are both from Braunstone, Leicester, were told by the city’s magistrates that they will appear next at its crown court on June 15.
Burder, 28, who wore a black polo shirt and blue jeans, and King, 27, in a grey sweatshirt and jogging bottoms, spoke only to confirm their personal details.
Neither was asked to enter a plea during the hour-long hearing before three magistrates.
Both men were arrested following the accident near Megan’s home town of Enderby, Leicestershire, on Sunday morning.
The rider of the motorcycle remains in hospital and his female pillion rider needed treatment too.
A third man has been arrested in connection with the case of Megan Bannister.
A 34-year-old man was arrested on Wednesday on suspicion of possession with intent to supply Class A drugs. He remains in police custody.