Jackett took the role on in January 2023, making a career transition after over 25 years in management.
However, the Gills have confirmed he has decided to step away from the job due to medical reasons.
Jackett said: “I want to thank Brad and Shannon [Galinson, owners] for the last couple of years, I’ve enjoyed working at Gillingham.
“In Mark [Bonner, manager], the club has a great guy managing the team and I’m sure he and the club will do well. I wish everyone the best of luck for the rest of the season.”
Brad Galinson said: “Kenny has been a calm and knowledgeable person to have around the club.
“His experience and contacts within the game have been invaluable and whilst we are sad to see him step down, Kenny’s health is the most important thing and must be his sole focus.
“I’m grateful for what he has given to the club and I’m sure our fans will respect his and his family’s privacy.”
Jackett is a vastly experienced figure in football and has managed the likes of Millwall, Portsmouth and Wolverhampton Wanderers.
He had a very brief stint in charge of Rotherham United, resigning just 39 days after his appointment.
Jackett was replaced as Millers manager by Paul Warne, who went on to spend six years at the helm before leaving for Derby County in 2022.
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