The new GCSE system in England is in danger of "further disadvantaging the disadvantaged", research for the social mobility charity Sutton Trust finds.
The study says grades for disadvantaged pupils fell slightly, compared to their peers, by just over a quarter of a grade across nine subjects.
These pupils were also less likely to get a 9 grade - with 1% achieving this compared to 5% of wealthier children.
The charity says ministers must monitor the long-term impact of the reforms.
The report - Making the Grade, by Professor Simon Burgess from Bristol University and Dave Thomson from FFT Education Datalab - assesses data from pupils at state-funded schools from 2016 to 2018.
It counts disadvantaged pupils as those "eligible for free school meals (FSM) at any point in the six years up to and including the year in which they reached the end of Key Stage 4".
The researchers say it is at the grade 5 boundary where most of the negative effect of the reform on disadvantaged pupils occurs.
"Non-disadvantaged pupils were 1.63 times more likely to achieve grade 5 or higher following the reform, whereas they were 1.42 times more likely to achieve grade C or higher beforehand.
"This will matter if grade 5 rather than grade 4 becomes the expected standard for progression to post-16 courses or even in university admission."
The researchers say 2% of disadvantaged pupils got the top grade A* under the old A*-G system, but just 1% got a 9 under the new numerical system, while for non-disadvantaged pupils, this stood at 8% and 5% respectively.
The report says: "Our central finding is that the reform has increased the GCSE test score gap between disadvantaged and non-disadvantaged pupils.
"The change is small, at an average of 0.02 standard deviations per subject, but is not trivial and is statistically significant.
"The results showed that the worsening of the gap is found among pupils with middle levels of prior attainment - those who were at Level 4 on average in Key Stage 2 reading and maths tests [Sats].
"The effect of the reform on disadvantaged pupils with higher levels of prior attainment was neutral."
It warns: "The overall result is clear: we find a statistically well determined effect, small but going in the direction of further disadvantaging the disadvantaged.
"So far at least, and although it could be argued that positive effects may take longer to come through, the GCSE reforms have widened the attainment gap, as young people move into the labour market or on to further study."
Reforms to GCSEs were introduced by Michael Gove in 2015, with the first cohorts taking the new exams in maths and English in 2017 and across a wider range of subjects from 2018.
The changes were a move from modules to a focus on final exams, and a change in the grading system from letters (A*-G) to numbers (9-1).
The aim was to improve standards by making courses harder, and increase differentiation at the top of the grade range.
Chief executive officer of the Sutton Trust James Turner said: "Our research tells us that the changes have likely had a small impact on the attainment gap, with disadvantaged pupils losing out by about a quarter of a grade across nine subjects.
"It will be important that the government monitors carefully the long-term impact that the reforms may have."
The Conservative government defended its record with Schools Minister Nick Gibb saying: "Conservative education reforms are improving standards in our schools, meaning children can get a better start in life."
Labour's Education Secretary Angela Rayner, Shadow Secretary of State for Education, said: "Labour will provide record levels of investment in our schools and increase education opportunities for every child, regardless of their background."
The Liberal Democrats did not respond to requests to comment on the report.
Geoff Barton, General Secretary of the Association of School and College Leaders, said: "The reality is that the students who struggle the most - many of whom come from disadvantaged backgrounds - have a very poor experience of the new GCSEs and leave school feeling demoralised about their prospects for onward progression to courses and careers.
"We are calling for an overhaul of GCSEs which improves the prospects of the forgotten third of students who currently fall short of achieving at least a grade 4 'standard pass' in GCSE English and maths."