The 32-year-old, who became Latics boss in March last year, will now remain at Boundary Park until the summer of 2017.
"I am loving working here, it's been an unbelievable topsy-turvy year but I am loving it," Johnson told Oldham's official website.
"I have been here around 10 months which places me about 40th in the list of long-serving managers, which shows the state of football at the moment.
"I have got greyer, grumpier and have put a bit of weight on, but I'm loving it - I love the club. The new contract extension makes me feel valued by the owner and the board. I know I will get it right and that I will be given time to do that, at what is a fantastic club."
Johnson's side are currently 17th in League One.