Difficulties with behaviour, emotions and socialising are more apparent in boys than in girls, the Department for Education has said.
Government statistics indicate that 17.2% of boys have special educational needs as a primary factor, compared with 6.2% of girls.
However more girls (22.6%) than boys (16.5%) have "moderate learning difficulties", according to the department.
Kent has the highest number of pupils with special educational needs, at 6,492. Birmingham has 6,119 and Essex has 6,086. All three local authorities are among the largest in the UK. The lowest figure is in Rutland at 207.
The department said earlier this year that, as of January, a total of 220,890 children at all state schools had their own statements of special educational needs, plus an additional 1.47 million pupils had more general special educational needs. This is almost a fifth (18.2%) of all state school pupils.