The 31-year-old Lancashire allrounder, who retired from test cricket after last month's Ashes victory with England, said the warmer climate would benefit the rehab process, which is overseen by former England physiotherapist Dave Roberts.
"It's always easier doing rehabilitation in warm weather and that's the main reason why we've decided to go to Dubai," Flintoff said.
Flintoff plans on beginning his training schedule within a week in an attempt to return in time for England's one-day matches in Bangladesh next year.
Meanwhile, Kevin Pietersen will miss next month's Twenty20 Champions League in India because of an Achilles injury. Pietersen was set to play for the Bangalore Royal Challengers.