The news was announced today (30 March) at a meeting of the 20 clubs of the top division of English and Welsh football.
Johnson joined the organisation aged 25 in December 2000 as a press officer. He worked his way up to become head of comms with a place on the executive leadership team in 2009, before becoming comms director in 2011.
He said he would now "take some time" to consider his next move.
Premier League executive chair Richard Scudamore said Johnson had "proved himself to be an outstanding communications professional, working in and then leading one of the busiest and highest-profile media departments anywhere in sport".
"He has made an important contribution to the Premier League’s reputation here and around the world and he leaves us with our very best wishes for the future," Scudamore added.
Dan Johnson said: "The Premier League is a fantastic organisation and it has been a privilege to grow and develop with it. There has always been a challenging range of issues on the agenda – from regulatory intervention to refereeing standards and everything in between – all played out in the glare of national, global and, ever-increasingly, digital and social media."
Calling the job an "all-consuming role", he went on to say: "I have decided that I need to take some time to consider what the next phase of my career might hold. There is no ideal time to leave the Premier League, but having built an effective communications function and helped lead, develop and implement our new brand and reputation strategy, the timing feels right."
Nick Noble, head of corporate comms, will deputise after Johnson's departure. The eight-person comms team also includes comms manager Alexandra Dallas and head of publicity Alastair Bennett. Dallas joined the league last year, having previously worked for Pitch Marketing Group.
Pitch has today emerged as the winner of an agency search reported by PRWeek last summer - the league was looking for a comms firm to work with it on community-related initiatives. The Premier League and Pitch today unveiled their first campaign since the relationship started in the autumn; an unsponsored TV ad created by Y&R London that showcases Premier League Primary Stars, a free curriculum-linked teaching resources for parents and schools.
At the start of last year, the league announced a new logo and visual identity designed to work better in the digital age (see below). It is the first time since the league's inaugural season that it has not had a title sponsor.
In his profile in the 2017 PRWeek UK Power Book, Johnson said that British world number one tennis player Andy Murray was the individual or organisation who had most adeptly managed their reputation in 2016, and said the PR industry should provide life-coaching to all its staff.