Imani Wiltshire was discovered on the lower deck of the bus in Stratford, east London, on 28 September.
She was taken to hospital where she was pronounced dead. A post-mortem examination found she died from head injuries.
Rosalin Baker, 25, and Jeffrey Wiltshire, 52, of Manor Park, pleaded not guilty to murder at the Old Bailey.
They also denied charges of causing or allowing the death of their child.
A trial date has been set for 13 March at the same court.
The parents of a three-month-old baby found seriously hurt on a bus have denied murder.