Pinkner has worked on the Fox sci-fi drama, along with Joel 'JH' Wyman, since its first season in 2008.
His decision to leave the show is "amicable" and will allow him to pursue other projects, TV Guide reports.
Fringe co-creator JJ Abrams said in a statement: "We're so excited to begin work on a fifth season of Fringe and to be able to deliver the 13 final episodes to our passionate and devoted fans.
"For four years, JH Wyman and Jeff Pinkner have worked tirelessly as a team to keep all the worlds in order on Fringe. We're thankful for the invaluable contributions Jeff has made to the show and of course wish him well and look forward to working together in the future."
He continued: "JH Wyman's importance to Fringe cannot be overstated, however, and I'm thrilled that he will continue as showrunner for the concluding chapters of our story. We can't wait for our fans to see what we have in store for them in the wild conclusion of Fringe."
Fringe will return to Fox on Friday, September 28 at 9/8c. In the UK, the series airs on Sky1.