The 29-year-old all-rounder returned to county duty with Lancashire last week after a third bout of ankle surgery in two years.
He is now set to make his international comeback during the seven-match one-day series at home to India, which starts on August 21.
Also included is fellow all-rounder Ravi Bopara, one of England's few successes from their disappointing World Cup campaign in the Caribbean. He missed the home one-day series against the West Indies, which England lost, earlier this season because of a thigh injury.
But England Test captain Michael Vaughan and Test opener Andrew Strauss have been omitted.
"Our squad for the NatWest Series against India contains the majority of the players chosen against West Indies earlier this summer," said England's chairman of selectors, David Graveney, who announced the squad at The Oval.
"We are pleased to welcome Ravi Bopara and Andrew Flintoff back to the squad and we will continue to monitor Andrew's rehabilitation from his ankle injury closely in the run-up to the tournament against India.
"India will be tough opponents in the 50-over game and the challenge for the team will be to demonstrate greater consistency in performance as we continue to build towards the next World Cup in 2011," said Graveney, who stressed the India squad was for the first four games of that series alone.
Fast bowler Chris Tremlett has been recalled after two impressive Test performances against India.
England have opted for several specialists in their Twenty20 squad.
The 15-man party which, like the one-day squad, is captained by all-rounder Paul Collingwood includes leg-spinner Chris Schofield - who after playing his only two Tests so far in 2000 underwent a slump in form and was ultimately sacked by Lancashire.
But, given a chance by Surrey last year, Schofield was the most successful bowler in domestic Twenty this season with 17, with a best of four for 12 against Sussex at Hove.
Luke Wright, the top scorer in this season's domestic Twenty20 competition with 346 runs at an average of 43.25, has been called up for his first taste of senior international cricket.
But there was no place in the Twenty20 squad for left-arm spinner Monty Panesar.
Twenty20 was pioneered amongst first-class sides in England and, earlier this season, England drew a Twenty20 campaign 1-1 at home to the West Indies.
"Having reviewed the team's performances in the Twenty20 matches against the West Indies, the selectors felt it was necessary to include a number of players with greater experience of this format of the game in the squad to go to South Africa," Graveney added at The Oval, where he announced both squads.
Paul Collingwood (Durham, capt), Ravi Bopara (Essex), Stuart Broad (Leicestershire), Andrew Flintoff (Lancashire), James Kirtley (Sussex), Darren Maddy (Warwickshire), Kevin Pietersen (Hampshire), Matthew Prior (Sussex, wkt), Chris Schofield (Surrey), Owais Shah (Middlesex), Ryan Sidebottom (Nottinghamshire), Jeremy Snape (Leicestershire), Vikram Solanki (Worcestershire), Chris Tremlett (Hampshire), Luke Wright (Sussex)
One-Day International squad for India series (first four games only):
Paul Collingwood (Durham, capt), James Anderson (Lancashire), Ian Bell (Warwickshire), Ravi Bopara (Essex), Stuart Broad (Leicestershire), Alastair Cook (Essex), Andrew Flintoff (Lancashire), Dimitri Mascarenhas (Hampshire), Monty Panesar (Northamptonshire), Kevin Pietersen (Hampshire), Matthew Prior (Sussex, wkt), Owais Shah (Middlesex), Ryan Sidebottom (Nottinghamshire), Chris Tremlett (Hampshire)