The annual census by the Scottish Council of Independent Schools (SCIS) shows there are 28,917 children in mainstream private schools, down 0.4 per cent on the previous year from 29,039.
Despite the marginal fall, SCIS said the figure was “remarkable”, given the impact of the prolonged economic downturn on family finances.
However, despite attempts to revive the fortunes of boarding schools, the number of pupils there fell by 1.2 per cent when compared with last year.
Earlier this year, SCIS launched a marketing drive to bolster the number of boarders in Scotland from overseas.
According to the figures, there are 3,185 boarding pupils, compared with 3,224 in 2012-13 and 3,300 in 2011-12.
Around one in every 20 children in Scotland attends an independent school, although the number in Edinburgh is nearer one in four.
While term fees vary, parents can pay around £30,000 a year for children to board at prestigious schools.