Irene Hamilton, who has held the post for the last seven years, is leaving for a new job with Manitoba Justice.
Hamilton will become the province's director of justice innovation and is tasked with "streamlining" the system.
Attorney General Andrew Swan says Mel Holley has been appointed as acting ombudsman.
Holley is currently the manager of ombudsman investigations.
Swan says an all-party committee will seek out a new ombudsman.