The Ukrainian leader did not explain why he was making the changes, which come at a critical juncture in the nearly four-year war with Russia.
Shmygal had only started working in the defence role last July.
Zelensky hopes to replace him with 34-year-old digital transformation minister Mikhailo Fedorov -- a relative political novice who is little-known to the Ukrainian public.
The appointments require approval from parliament, though it has largely coalesced around Zelensky since Russia's invasion and is unlikely to torpedo his decisions.
Announcing Saturday's decision in a post on X, Zelensky said he hoped Shmygal would use his "systematic" approach to the defence role in the energy portfolio.
"I am counting on parliamentary support," he said.
Zelensky separately on Friday announced a new chief of staff, after his previous top aide resigned in November over a corruption scandal.
bur-cad/cw
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