MANCHESTER — Alyson Pitman Giles will be leaving Catholic Medical Center after 13 years as president and chief executive officer of the West Side hospital, the hospital announced Thursday.

In a single-page statement, the hospital said Giles and the hospital are “transitioning to a new leadership team.” Giles said she would remain employed until June 30 as a transitional consultant.

Dr. Joe Pepe, chief of medicine at CMC, will be interim chief-executive while a permanent replacement is sought. Manchester Bishop Peter Libasci said he approved Pepe’s nomination to the post.

“It is with both a light and heavy heart that I am stepping down today as Catholic Medical Center’s president and CEO,” Giles said in a memo distributed to staff at CMC and allied practices Thursday.

“I look forward to helping and identifying an individual who will embrace our mission, Catholic identity and love of our CMC family,” she wrote in the memo.

Hospital spokesman Morgan Smith said Giles will be an “off-site resource” and not have an office at the hospital. She referred all other questions to board chairman Guy Chapdelaine. A message left at his home was not returned Thursday night.

In the statement, Chapdelaine said Giles has been an incredible visionary.

“The hospital has exceeded expectations under her leadership,” he said. “We know her team has admired her spirit and dedication, and thank her for her past contributions to CMC. We are pleased she will continue to be available as a resource to the board.”

Giles took over at CMC in late 1998, as the merger that created a single hospital entity in Manchester, Optima Health, disintegrated.

CMC had lost its operating rooms, maternity center and many of its workers to its crosstown rival, Elliot Hospital.

Giles cut ties with the Elliot, beefed up the New England Heart Institute and slowly reestablished a surgery department and maternity ward. She expanded the McGregor Street hospital campus more than four-fold.

The employee roster went from 600 to 2,100 under her tenure.

Throughout the time, Giles cultivated the CMC brand, appearing in advertisements and promotional activities.

“She was good at marketing,” said one of her critics, pro-life activist Barbara Hagan.

The New Hampshire Union Leader reported in 2010 that Giles’ compensation totaled $1.36 million the previous year.

The number was inflated by a one-time retention bonus and deferred compensation. But the high figure led critics to question why a Catholic charity would pay so much. Smith referred questions about severance pay and deferred compensation to Chapdelaine.

Later in 2010, Attorney General Michael Delaney objected to a so-called affiliation between CMC and Dartmouth-Hitchcock, an initiative Giles had said was essential for the hospital’s future.

Hagan said she wishes Giles well, but said the hospital has to return to its Roman Catholic mission.

“It can’t get caught up in worldly goals,” she said. She expects that Libasci will play an active role in selecting a replacement.

In a prepared statement, Libasci said he met with Pepe and was assured of the physician’s commitment to promoting the mission and Catholic identity of the hospital.