Two-thirds of England's schools face real-term budget cuts during this Parliament, according to the Institute of Public Policy Research (IPPR).
It comes as a newspaper report says the Department for Education is to be hit with £2bn worth of spending cuts.
The DfE has not yet commented on the report.
This year schools in England received £623 for every pupil on free school meals - a total of £2.5bn by the end of this Parliament.
Jonathan Clifton's analysis for the think-tank of how schools use the coalition's flagship pupil premium argues that it is "not additional money" for the majority of schools.
He said: "Over the next three years, schools face a cut in their main budget on the one hand, and an increase in their pupil premium funding on the other.
"The Institute of Fiscal Studies has calculated when these are taken two things are taken into account, the majority of schools are expected to see a real-terms cut in their per-pupil funding.
"They conclude that around 65% of primary schools and 80% of secondary schools will see a real-term cut in their budget between 2010-11 and 2014-15."
At the same time a minority will see a substantial increase in their budgets, it says.
He continued: "Many schools are struggling to maintain their existing level of provision, and are unable to fund additional or innovative activities.
"Perhaps unsurprisingly, those schools that report they have 'significantly' changed the way they support disadvantaged pupils tend to be the same schools that have seen an increase in their budget."
The fact that the pupil premium is not ring-fenced means that is "subject to competing demands", and the school league tables system often means schools focus their resources to ensure pupils get at least C grades in GCSEs.
He also highlighted how politicians talk interchangeably about the pupil premium being used to support pupils who are falling behind and those on free school school meals.
But last year only 23% of low attaining pupils at the end of primary school were on free school meals, and only 26% of pupils on free school meals were low attaining.
He also calls for the extra funding to be tied to a strong professional infrastructure to ensure the best results are achieved.
The report calls for the greater share of the money to be re-targeted at primary schools to ensure that more pupils are starting secondary school with adequate standards in English and maths.
It also suggests that money aimed at secondary school pupils who are falling behind, known as the "catch-up premium", should be re-named a "catch-up entitlement" to ensure it reaches the correct pupils. BBC News