Archer has been struggling with the problem throughout the India tour and missed two of the four Test matches which preceded the white-ball leg.
England have named a 14-man squad for the three ODIs, all of whom were already in India as part of the T20 touring party, with three more players – Dawid Malan, Chris Jordan and Jake Ball – staying on as reserves.
An ECB statement said: “Jofra Archer is returning to the UK for further management and investigation of his right elbow injury.
“Jofra’s elbow issue has deteriorated over the course of the Twenty20 International series and made it increasingly challenging for him to maintain performance levels. He has been deemed unfit for selection for the ODI series that features matches on 23, 26 and 28 March.
“The ECB medical team will assess the player and, together with Jofra, develop a treatment plan and a return-to-play schedule in due course.”
The statement also confirmed that Archer would miss the start of the Indian Premier League season, where he was due to star for the Rajasthan Royals, having been named MVP at last year’s tournament.
As well as Archer, England are without World Cup winners Joe Root and Chris Woakes, who are being rested after their involement in the Test tour of the sub-continent.
England Men’s ODI Squad: Eoin Morgan (Middlesex) (captain), Moeen Ali (Worcestershire), Jonathan Bairstow (Yorkshire), Sam Billings (Kent), Jos Buttler (Lancashire), Sam Curran (Surrey), Tom Curran (Surrey), Liam Livingstone (Lancashire), Matt Parkinson (Lancashire), Adil Rashid (Yorkshire), Jason Roy (Surrey), Ben Stokes (Durham), Reece Topley (Surrey), Mark Wood (Durham).