That series also marks the start of a new World Test Championship cycle.
Brathwaite, 32, led West Indies in 39 Tests after replacing Jason Holder as captain during the pandemic.
On his watch the West Indies won or drew nine of 16 series.
They beat England at home in 2022, and won in Australia for the first time in 27 years in Brisbane in 2024. In his last game as captain, in January, West Indies ended a 34-year drought in Pakistan.
Brathwaite has played 98 tests, the last 88 in a row since 2014, eclipsing Garfield Sobers' national record streak, but the job appeared to increasingly weigh on his batting.
His 54 in Multan in January, when he went after the Pakistan spinners, helped to set up an historic 120-run series-levelling win, but it was first half-century in 13 innings, and third half-century in two years.
"Kraigg Brathwaite has been an outstanding leader for our test team, guiding the squad with discipline, resilience, and a deep understanding of the game," West Indies director of cricket Miles Bascombe said.
"His contributions have been invaluable, and under his leadership we have witnessed historic moments that will be remembered for years. We thank Kraigg for his service as captain and look forward to his continued impact as a senior player."
A replacement is yet to be appointed, but wicketkeeper-batter Shai Hope, 31, has been named West Indies Twenty20 captain taking over from Rovman Powell, who had led the T20 side since 2023.
Hope is already West Indies' one-day international skipper.
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