Fletcher, who wants a fresh squad for the first of five Ashes Tests against Australia starting in Brisbane on November 23, is worried his players may be tired when the Champions Trophy ends on November 5.
"We will look to see who will need a rest before going to Australia and we will make plans accordingly," Fletcher said ahead of Wednesday's fifth One-dayer against India here.
"We will have to look at the Champions Trophy and see what our attitude is towards it."
With India having already clinched the One-day series with a 4-0 lead, Fletcher is considering leaving out captain Flintoff for the last two matches.
"We want to give Freddie a rest whenever we can," Fletcher told reporters. "We'll monitor him as the tour and the summer progresses.
"I'm looking at all the players all the time. That's why I'm pulling guys out because I'm looking at September when people are just looking at the next week.
"You've just got to look quite a long way away down the line."
When England return home after the final One-dayer in Indore on Saturday, they will have less than a month off before the first Test against Sri Lanka starts at Lord's on May 11.
England face a gruelling home season with three Tests against Sri Lanka and four against Pakistan and five one-dayers each against both countries.
This will be followed by the Champions Trophy in October-November, the tour of Australia from November-February and the World Cup in the West Indies in March-April.
The International Cricket Council, which organises the Champions Trophy every two years to raise funds for its development activities, insists on every country fielding its best team.
But teams have in the past cited injuries to keep players away from the action.
The biennial tournament, regarded as a mini World Cup, features the six top limited-overs teams as on April 1, 2006 and two qualifiers drawn from the remaining four Test-playing nations.
England have been drawn with world champions Australia, hosts India and a qualifier in group A of the main tournament.
The other group comprises South Africa, Pakistan, New Zealand and the top qualifier.
Two teams from each group will make the semi-finals. The final takes place on November 5.
The West Indies won the last edition of the Champions Trophy two years ago defeating hosts England in the final.