A survey by The Herald shows fees will increase by an average of nearly four per cent for the 2014/15 school year - with the highest fees topping £25,000.
Over the past five years fees in the independent sector have risen by around 15 per cent, with the average annual cost to families climbing from £11,410 in 2010/11 to its current figure of £13,103.
In June, the consumer price index, the Government's preferred measure of inflation, was running at just 1.9 per cent while the retail price index rose to 2.6 per cent.
The most expensive independent school in Scotland is Gordonstoun, in Moray, where Prince Charles was educated, which will charge £25,392 a year for a senior school day pupil, after a three per cent rise.
The second most expensive school is Fettes College, in Edinburgh, whose former pupils include Tony Blair, which increased its fees by 4.6 per cent and now charges £23,190.
Fees for Merchiston Castle School in Edinburgh are the third-highest in our survey, at £21,045 after a 4.2 per cent increase.
In Glasgow, overall increases have been varied, with parents from Hutchesons' Grammar School seeing one of the lowest increases of just 1.9 per cent, bringing the fee to £10,430.
A spokeswoman for the school said: "Sound financial management has resulted in fees that remain amongst the lowest in Scotland, while ensuring our excellent results, facilities, curriculum and staff continue to be at the forefront of Scottish education."
One of the highest increases in the country was the 6.9 per cent rise at St Aloysius' College which saw fees climb to £10,314. Fees at Fernhill, in Rutherglen, which narrowly escaped closure this year, also saw a significant rise by 8 per cent, although they remain amongst the lowest in Scotland.
St Aloysius' College headmaster, John Browne, said: "In order to maintain and enhance the depth and breadth of the curriculum and to ensure a strong future for the college, the governing body took the decision to increase fees.
"Taking account of the financial implications for our parents, the college has taken a number of measures to limit the impact of the fee increase, including a wide ranging review of costs to ensure the most effective use of resources.
"It is important to ensure that the college has a solid financial base from which to thrive and develop, which will allow our pupils to do the same."
The fee rises come at a time when the cost of a private education is under the spotlight because of the recession.
The number of children attending private school in Scotland has fallen, with a drop of 1.5 per cent in both nursery and primary between 2010/11 and 2011/12.
In 2013 some 31,146 children attended private schools in Scotland, around 4 per cent of the total pupil population.
John Edward, director of the Scottish Council of Independent Schools, argued recently that all schools worked hard to keep fees to a minimum - and to help any families having difficulty with fees. He highlighted figures that show Scottish private schools have spent millions of pounds on extra bursaries for pupils from poorer backgrounds in recent years.
Two years ago, £32 million was spent by the independent sector on pupil grants compared with £24m the previous year - a rise of 33 per cent. Four years ago just £17m was spent.
Earlier this week a study showed families are now paying more than £500,000 to give a private education to two children.
The Killik Private Education Index also shows the soaring cost of private education since 1990, with average fees across the UK having more than quadrupled.
It also found the cost of extra-curricular activities as well as uniforms and sports kit have increased from an average of £1,200 a year in 1990 to £3,000 in 2014.
Sarah Lord, managing director of Killik Chartered Financial Planners, said: "For any parent considering private education for their children, the results of this study will prove very alarming."