The ECB recently stated that the all-rounder was available for selection after being absent since September.
Stokes was not considered by the selection committee while he was under investigation by the police in relation to a brawl outside a Bristol nightclub four months ago.
The 26-year-old has since been charged with affray and will be the subject of a hearing at Bristol Magistrates' Court on February 13.
Despite being free to play for England, Stokes has decided not to make himself available until after the court date.
The Durham cricketer tweeted: "As has been confirmed in the media a first hearing date at court has been set for 13th February. In the circumstances, I have decided that it would not be right to join my teammates until after attending court on the 13th."
England will face Australia in a Twenty20 series in February before taking on New Zealand in all three formats.