The decision came after the 4-2 defeat at home to Swindon on Monday with Keith Peacock placed in caretaker control.
In a statement released through the League Manager's Association, Parkinson said: "Naturally I am very disappointed to be leaving Charlton Athletic. This campaign has proved to be extremely competitive, with only a few points separating several clubs.
"I firmly believed in the players' abilities to improve on last season's finish and again compete for promotion back to the npower Championship.
"I would like to take this opportunity to wish the club, the management, the players and the supporters all the very best for the future. I now look forward to a new challenge in the game."
Richard Bevan, the LMA chief executive, said: "It is extremely disappointing that Phil has become the next manager to get the sack in this new year period. Charlton are losing a young, talented manager, whom at the age of 43 has already managed over 300 games. Without a doubt Phil will take his knowledge and skills to another club where I am certain he will be a success."