Chirlane McCray’s signature mental health initiative, ThriveNYC, has a sky-high staff turnover rate of over 40% since its August 2016 inception — even though the average salary is a hefty $104,000.

Of the 41 total positions ThriveNYC has created over the past three years, 17 employees have left their jobs.

The average time a ThriveNYC staffer stays in their position is just 10.5 months, and 16 people are new to the initiative within the last year alone.

A former staffer said the $1 billion plan — which has been criticized for its lack of transparency and results — has had a muddled mission and message, leading to an early exit by many frustrated employees.

“I think a lot of people are there for a mission that hasn’t always been clearly and consistently stuck with,” the ex-staffer said, faulting ThriveNYC’s leadership for failing to communicate goals clearly to the public, the press and elected officials.

ThriveNYC’s abysmal retention rate is even lower than the average tenure of employees at the city’s Administration for Children’s Services that handles emotionally-fraught cases of neglected and abused kids.

Most ACS caseworkers stay on the job for three years — triple the length of their Thrive counterparts, according to a 2017 City Council report.

“Our mental health system is a failure. A lot of people came with the commitment to really change the system and reform it and innovate it — and sometimes doing the work for that can take awhile,” said the former Thrive employee.

“There may have been some second guessing on how much to put that aspect front and center. People may have become frustrated with that hesitancy.”

The pressure of politics, including a probe by City Comptroller Scott Stringer, has also damaged morale at ThriveNYC.

“There’s expectations to show results very quickly in ways that may not be realistic,” the former staffer said, adding that the lynchpin mental health program of Mayor Bill de Blasio’s administration has not lived up to its potential.

“That’s been disappointing to people who came to work for it with big expectations.”

ThriveNYC hasn’t faltered for lack of resources.

The initiative’s staff budget has ballooned from $1.6 million in the first year to $2.6 million as of October. An executive assistant to director Susan Herman makes $93,000 a year, while Herman’s salary is the highest at $233,000 — a big jump from her predecessor who made $195,000.

A City Hall spokeswoman defended ThriveNYC’s staffing.

“Thrive employees — tasked with improving mental health for all New Yorkers — do some of the most meaningful work we can do as government. It is hard and strenuous work, and we’re thankful for every day they do it,” said de Blasio’s Press Secretary Freddi Goldstein.

Goldstein added that some turnover was due to the fact that ThriveNYC just created its first central office in January.

She said the majority of people who’ve been at Thrive for less than a year were hired when the new office was opened and are still in their positions.

When those tenures are removed from the equation, the average duration of employment has been 18 months, Goldstein said. Their salaries are commensurate with other city employees, she said.