He said it was unfair that East Riding schools in his constituency receive £400 less per pupil than those in neighbouring Hull.
The former education select committee chairman has now joined the f40 group campaigning on behalf of schools in areas which get the least cash per pupil in the country.
Last year the coalition Government announced £390m would be spent narrowing the gap between the best and worst funded areas.
Now Mr Stuart is calling for more to be done after talks with education and childcare minister Sam Gyimah.
He said: “It is morally indefensible that children in places like East Yorkshire continue to receive over £400 less for their education each year than children on the other side of the authority boundary in Hull.
“Enormous variations like these, which are replicated across the country, are not based on need, but are the result of an unfair funding system.”
He added: “Last year Ministers committed an extra £390m to help reduce some of the unfairness in school funding. This was good news, but I continue to have concerns about how this extra resource was allocated and I also want to hear Ministers confirm that this will not simply be a one-off payment. The ultimate goal, however, is to see a new National Funding Formula introduced.”
At the first education questions of the new Parliament last week Education Secretary Nicky Morgan said it was “clearly unfair” that a school in one part of the country could attract over 50 per cent more than an identical school elsewhere.
She said the Conservatives had committed to making school funding fairer in their election manifesto and “would come up with proposals in due course.”