A total of 335 staff at the university are on wages of £100,000 or more, placing Edinburgh first in the rankings.
Glasgow University was fourth with 246 staff earning in that wage bracket, with Dundee ninth with 133 employees on £100k or more.
The rankings were compiled by the Taxpayers' Alliance and based on figures of the number of high earners across 2016/17, 2017/18 and 2018/19.
Oxford and Cambridge universities did not provide the full information requested and were excluded from the rankings.
Taxpayers' Alliance spokesman Keiran Neild said: "These rankings shine a light on the thousands of university administrators taking home very plush pay packets."
He added: "Instead of constantly complaining about faculty budget cuts, uni bosses need to get their bumper wage bills under control and focus with providing their students with the very best higher education they can."
A spokesman for Edinburgh University told the Scottish Daily Mail: "The University of Edinburgh is a world-leading institution that sustains its high academic standing through the quality and distinction of its staff"
"The university is in competition for these staff with other leading world institutions, so it is necessary to offer remuneration packages that enable us to attract and retain the very best staff."
The top ten ( number of staff on £100k or more)
1. Edinburgh 335
2. Manchester 331
3. Cardiff 250
4. Glasgow 246
5. Queen Mary 207
6. City University 178
7. Newcastle 159
8. Leeds 158
9. Dundee 133
10. York 127