Test captain Stokes, who has not played an ODI since the 2023 World Cup, had said he was open to returning to the white-ball set-up following Brendon McCullum's appointment as head coach across all formats in September.
However, the 33-year-old was not included in a 15-man party announced by the England and Wales Cricket Board on Sunday having suffered a recurrence of a hamstring problem during the recent Test series in New Zealand.
Stokes previously missed the summer series against Sri Lanka and the first Test against Pakistan in the autumn due to hamstring issues.
"Durham allrounder Ben Stokes was not considered for selection as he continues to be assessed following a left hamstring injury sustained during the third Test match against New Zealand earlier this month," statement read.
Ben Stokes clutches at his left hamstring during the recent third Test in New Zealand. (AP PHOTO)
Joe Root does return to the squad having been away from the international white-ball scene for over a year and Jos Buttler is back as captain after missing the ODI team's most recent series in the West Indies.
Liam Livingstone, who impressed as skipper in Buttler's absence, returns to the ranks but Sam Curran, Will Jacks and Reece Topley all miss out after failing to further their claims in the Caribbean.
Jofra Archer did do enough to prove his fitness and fellow seamer Saqib Mahmood is included despite limited opportunities.
Jacob Bethell features having impressed in the Test arena in New Zealand.
The squad will also play five T20 internationals and three ODIs in India from January before travelling to the Champions Trophy in Pakistan.
Spinner Rehan Ahmed will feature in the initial T20 leg of the tour before dropping out, while Root will only link up with the squad when the ODI programme begins.
ENGLAND SQUAD FOR ODI SERIES IN INDIA AND ICC CHAMPIONS TROPHY:
Jos Buttler (capt), Jofra Archer, Gus Atkinson, Jacob Bethell, Harry Brook, Brydon Carse, Ben Duckett, Jamie Overton, Jamie Smith, Liam Livingstone, Adil Rashid, Joe Root, Saqib Mahmood, Phil Salt, Mark Wood.
* Rehan Ahmed to feature in T20 series in India, with Root not involved.
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