Albyn School in Aberdeen was named best in the independent sector for Advanced Higher results, followed by St Margaret's School in the same city and St George's School in Edinburgh.
Experts claimed the results were proof of the benefits of single-sex education.
A table based on A-level results places Edinburgh's Fettes College top, with St George's in second place and St Leonard's School in St Andrews third.
The league tables, which are the first of their kind for the independent sector in Scotland, were drawn up by the website best-schools.co.uk. Previously the site only produced tables for England and Wales.
Les Webb, the managing director of the company which produces the website, said they had decided to draw up the Scottish table following demand from parents.
He said: "I am forever getting complaints from parents in Scotland saying we ignore Scotland and no-one else publishes these results.
"The Scottish Executive seems to go out of its way to avoid anything which resembles a schools league table.
"Private schools are often quick to play down these league tables, but the fact remains that 600 parents visit this website every day.
"It just reinforces how much importance parents place on academic track records of schools they wish to consider for their children."
The tables are based on the percentage of pupils gaining an A or B pass at either Advanced Higher or A-level.
Schools which presented fewer than 20 candidates for the exams, or who only offered a limited range of subjects, were not included in the calculations.
Although Albyn School announced last year that it was going to start accepting boys for the first time, it was still an all-girls school when pupils sat their exams last year.
Albyn's headmaster, Dr John Halliday, said he was "delighted". "The combination of small classes and a purposeful academic environment has reaped benefits," he said.
Lyn McKay, the headteacher at St Margaret's School, said the results were proof that girls work best in a school with no boys.
She said: "It's common knowledge that girls have different learning needs from boys, and if girls are in a single-sex school the teachers can focus on a special way of teaching that enables girls to do their best.
"At St Margaret's we have small classes and our timetable is built around the girls' choices, allowing the girls to follow their particular strengths.
"We also have a very good reputation for art, music and sport, which are all things which help to boost girls' self-esteem."
But Fiona Valpy of the Scottish Council of Independent Schools said parents look for more than just exam results when choosing a school for their children.
She said: "Parents look for things like the amount of individual attention their child will get and the type of facilities the school offers before they look at academic performance."