Life isn’t getting any easier for Athenahealth’s Jonathan Bush.

As the health care CEO fends off a takeover attempt by activist investor Elliott Management, Bush is being forced to face a second allegation of his mistreatment of women.

Bush was accused of ogling the breasts of a female employee and “making comments about his sex life,” documents reviewed by The Post reveal.

In the March 2009 case, filed also against the company, the female employee, who reported directly to Bush, also accused him of making “sexually oriented remarks” about her and other female employees, the civil complaint, filed with the Massachusetts Commission Against Discrimination alleges.

The MCAD is the state agency charged with enforcing discrimination cases.

No longer willing to deal with Bush’s behavior, the employee left the company in 2008 — even though the exit meant forfeiting her “IPO bonus” — a cash payout tied to Athenahealth’s September 2007 initial public offering, she claimed.

The case was quickly settled two months later, according to documents filed with the agency. Terms of the settlement are not public.

When reached by The Post on Thursday, the woman — whose name is being withheld by The Post — declined to discuss the settlement terms.

“It was a complicated situation,” she said, noting that Bush is “a friend.”

“He’s a good man, a good leader, it’s a great company,” she added.

Athenahealth said it works hard to ensure an inclusive work environment — and in recent years updated its harassment and discrimination policy to require training seminars for all employees.

”Like almost any public company, Athenahealth has been the subject of various employment-related claims from time to time,” the company said in a statement issued to The Post.

Earlier this week, London’s Daily Mail obtained 2006 court documents in which Bush confessed to “numerous physical altercations” with then-wife Sarah Seldon.

Bush, who is a nephew of former President George H.W. Bush and a cousin of former President George W. Bush, has since apologized.

“I take complete responsibility for all these regrettable incidents involving my dear former wife. … I accept responsibility for my conduct and apologize to everyone involved,” he said in a statement Tuesday.

The past court cases outlining Bush’s behavior toward women could affect Athenahealth’s battle with hedge fund Elliott Management.

The $35 billion fund, which usually prods companies to make changes, has taken the somewhat unusual tack of trying to buy the company in a $6.9 billion all-cash deal.

Reps from Elliott declined comment.