Council chief executive Andrew Kerr took home the top basic pay of £167,468 - bolstered to £203,139 with pension contributions.
While Lothian Buses managing director Richard Hall’s £227,700 bumper pay packet was made up of £165,000 salary plus bonuses and pension add-ons.
A council spokeswoman said: “We want to promote transparency and accountability within the council and always publish the salaries and expenses of our most senior managers as part of our annual accounts.
“The majority of individuals identified in this report are, however, not directly employed by the council.
“For those who are, salaries are determined by a job evaluation scheme and reflect the level of responsibility required by the roles concerned.”
Mr Hall’s salary was boosted by a £46,200 bonus and pension contributions of £16,500.
Lothian Buses are currently recruiting trainee drivers on £24,000-a-year while existing staff are threatening strike action over a “hostile” management culture.
Jim McFarlane, Lothian Buses chair, said: “Lothian’s salary packages are benchmarked and set in comparison to other transport providers so that leadership talent can be found and retained.
“This in turn assists Lothian in maintaining its high levels of business performance, innovation and customer satisfaction as well as its position as offering the most value for money service in Scotland.”
Also earning more than Nicola Sturgeon are council executive directors for planning and transport, Paul Lawrence, and social work, Alistair Gaw, both on £150,390.
The cash-strapped council is currently looking to cut around 200 jobs as it makes £33 million worth of savings over the next year.
Completing the list are Transport for Edinburgh chief George Lowder on £141,800, Marketing Edinburgh boss John Donnelly on £139,200 and Edinburgh International Conference Centre head Marshall Dallas on £139,138.
First Minister Nicola Sturgeon’s yearly wage is £135,605 after she and fellow cabinet members opted to freeze it for a decade.
Another four public sector bosses in the Capital are paid six-figure salaries.
John O’Connell, of the TaxPayers’ Alliance said: “Families in Scotland who work hard to pay their council tax will be furious that so much of their money is just going towards these high salaries.”