In Avengers: Endgame, as all the stones were returned to their timeline, will Doctor Strange have the time stone now?
Yes and no.
Since all the stones are returned back to their original time and place in the end, everything will go as they were. Dr. Strange will come to Sanctum, meet the Ancient One, become Sorcerer Supreme, and possess the time stone.
However, he will not have the Time Stone after the events of Endgame cause they are destroyed already.