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.

However, the Bairns boss has underlined that any forward signing will need to exhibit even more quality than two of his promising youngsters.
"If I bring another striker in he's got to be better than young Botti Bia-Bi and Scott Shepherd," said Houston.
"I would be looking for the more experienced type, and another defender would come in handy as well."
Eighteen-year-old Bia-Bi, a London-born Scot who has progressed through Falkirk's academy, glanced in a fine equalising header against Cowdenbeath on Saturday to ensure Houston's side left Central Park with a point.
The former Dundee United manager stated in no uncertain terms that he wants to "eradicate" the errors that allowed Cowdenbeath to lead twice in their first Championship game of the season.
Houston labelled "not picking up runners" as the problem for conceding the opening goal and a "crazy mix-up" as the reason former Bairn Sean Higgins gave the Blue Brazil a second.
An "exceptional" Rory Loy strike and Bia-Bi's header kept Falkirk on level terms.
"To score a header like that is not the easiest thing," added Houston. "He put it right in the corner so credit to him.
"He made an impact when he came on and he might be due a longer run from the start.
Next up for the Bairns is the visit of Rangers on Friday.

The service is available to Three customers travelling to the Republic of Ireland, Australia, Italy, Austria, Hong Kong, Sweden and Denmark.
European authorities have been clamping down on roaming charges.
But Three is the first network to abolish them altogether, albeit in selected countries, where it has sister networks.
Three says customers on a pay monthly contract would be able to use their allowances of free minutes, texts and data with no extra charges for being abroad.
However, those on unlimited plans will be subject to some restrictions.
In a press release, Thomas Malleschitz, marketing director at Three, said: "By abolishing expensive roaming charges in select countries, we are allowing our customers to get even more value from their minutes, texts and data abroad by removing the fear associated with staying in touch while travelling."
Analysts say that other operators of mobile phone networks are likely to follow Three's lead, particularly those who already have a presence in other countries.
Matthew Howett, a senior analyst at consultancy firm Ovum, says the deal from Three is also interesting because it applies to nations outside the European Union, where there has been pressure from authorities to lower roaming charges.
"Reducing roaming charges outside of that bloc will welcomed by many, since prices have remained stubbornly high in some countries," he said.

26 January 2015 Last updated at 09:11 GMT
The trees were part of an area known as 'Doggerland' which formed part of a much bigger area before it was flooded by the North Sea.
It was once so big that hunter-gatherers who lived in the area could have walked to Germany, in Europe, across its land.
The underwater forest was discovered by Dawn Watson and Rob Spray from Sea Search on a diving trip to study marine life.
The prehistoric forest lay undiscovered until it was exposed by the extreme storms along the east of England coast in December 2013.
Check out this underwater footage of the forest which experts believe could date back more than 10,000 years.
Underwater diving footage is copyright and courtesy of Rob Spray and Dawn Watson.

A selection of your pictures of Scotland sent in between 3 January and 10 February. Send your photos to scotlandpictures@bbc.co.uk or our Instagram at #bbcscotlandpics
The parents of a three-month-old baby found seriously hurt on a bus have denied murder.
[NEXT_CONCEPT]
Peter Houston is still seeking to fine-tune his Falkirk squad, with a striker and defender pinpointed as priorities.
[NEXT_CONCEPT]
Three has announced that it has abolished international roaming charges in seven countries.
[NEXT_CONCEPT]
Nature experts have discovered an amazing underwater forest thousands of years old under the sea close to the Norfolk coast in England.
[NEXT_CONCEPT]
All pictures are copyrighted.