Yorkshire and Humber suffered a bigger drop in transport spending per head from 2016-17 to 2017-18 than any other region in England, the IPPR North research showed.
Last year, public spending on transport in Yorkshire and Humber was Â£315, more than three times less than the Â£1,019 spent in London.
And since 2014, when the Northern Powerhouse project was initiated by the Tory-led coalition, transport spending per person went up twice as much in London than in the North as a whole.
The study comes following a year of rail misery in the North, with passengers left with unprecedented and unacceptable levels of delays and cancellations, and after London's Crossrail was delayed with costs over-running by Â£600m.
Bradford South MP Judith Cummins said: "The Government pays lip service to the Northern Powerhouse and giving the North the funding it needs, but in reality the story remains the same - cash funneled to London and the South East while we make do with what’s left over.
"The people and businesses that use public transport here every day will not be surprised at these figures.
"It is particularly depressing to see funding fall in Yorkshire - our region is being held back by this Government. I will continue to press this Government to address this wholly unfair situation."
Conservative former Transport Minister Robert Goodwill backed the Government for putting "unprecedented" money into infrastructure projects, but insisted Yorkshire needs "our fair share of this".
The Scarborough and Whitby MP said: "This is precisely why we need to get local projects in the pipeline.
"Previously massive projects such as Crossrail in London have skewed the figures but as that is nearing completion now is our opportunity to get rail and road projects into the schedule.
"This Government is putting unprecedented investment into infrastructure projects with, for example, Â£48bn for rail alone.
"HS2 is also a project that will bring amazing opportunities to cities in Yorkshire. All we ask is for our fair share of this."
Shadow Rail Minister and York Central MP Rachael Maskell said: “These figures expose the poverty of transport investment and widening inequality in the North and in Yorkshire in particular.
"Under the Tories, promised investment has been scrapped, downgraded or delayed at the same time as spending in our capital has increased. Labour will put an end to chronic underinvestment across the North, including spending at least Â£10bn to transform East-West northern rail links and boosting public transport investment.”
IPPR North warned that passengers are suffering the effects of years of under-investment, and renewed its call for the Department for Transport to invest in the North and devolve power over the region's infrastructure to Transport for the North.
Senior research fellow Luke Raikes said: “Today’s figures show us that government still needs to follow through on their promises to make the Northern Powerhouse a reality.
“An increase in spending in the North West in the past year is very welcome, as is the Â£37m announced in the Budget for transport in the North.
"But the North East and Yorkshire and the Humber are yet to see such a boost, and investment in the North still pales in comparison to spending in London.
"People are continuing to suffer the very real effects of decades of under-investment, and the ongoing chaos on northern trains is a clear sign of how far there is to go.
“The Northern Powerhouse has the potential to improve the whole country by transforming the North’s economy. In realising this, transport has an important role to play in helping to connect people, services and goods across the region.
“Next year will offer the Government an opportunity to improve their record on transport spending. They must take it.
"Transport for the North is now developing investment plans that will address this long-standing problem and the Government will then have the chance to follow through on their promises: to give the green light on long-overdue investment in the North; and to devolve real power so that the North can take responsibility for its own transport network.”
A Department for Transport spokeswoman said: “This Government is delivering a record Â£13bn to transform transport across the north by 2020. We are investing heavily in strategic roads for the Northern Powerhouse, spending almost Â£3bn to make trips faster and more reliable for both people and freight. Projects include the M62 between Leeds and Manchester which is being upgraded to a 4-lane smart motorway.
“Our priority is to boost economic growth by cutting journey times, increasing the number of seats on trains and improving the region’s road network.”