The gulf between the proportion of working class boys and girls attending university widened in the first year of the tuition fee hike, according to new research.
It suggests that male students from the most disadvantaged areas of England appear to be increasingly less likely to study for a degree.
Will Hutton, chair of the Independent Commission on Fees, which conducted the study, said that there has been a "worrying" widening of the gender gap.
The study analysed UCAS data on the numbers of students accepted on to university courses between 2009 and 2012.
Tuition fees were trebled in 2012 with English universities allowed to charge up to a maximum of £9,000.
The findings show that in the 40% of English neighbourhoods where teenagers are the least likely to go to university, around 1,700 fewer boys aged 19 and under were accepted on to degree courses in 2012 than in 2011.
The fall is partly down to changes in the population, the report says, but adds that the drop represents a 5.4% decline in the numbers of young male students from these areas going to university.
There was a smaller drop, around 3.7%, in the number of female students aged 19 and under from these neighbourhoods being accepted on to university courses, it adds.
The study says that the decline in boys from all backgrounds going on to higher education is "notable". Between 2010 and 2012, there was a 6.2% drop in boys from the richest neighbourhoods going to university, and a 1.4% drop in boys from the poorest.
It adds that while the decline was bigger among boys from the richest areas, there are still 20,000 more male students from these areas going to university each year than those from the poorest backgrounds.