Towler has been with UKIP in various roles since joining in 2004, initially in Brussels and latterly in London.
He will remain in post until the party's extraordinary general meeting on 17 February, after which he will continue to be a media consultant to the party on a part-time, freelance basis. It leaves the party without any press officers.
Towler's departure comes as UKIP faces internal turmoil due to racist texts sent by the former girlfriend of leader Henry Bolton - and doubts over Bolton's claim to have ended their relationship. The party's executive committee has since passed a vote of no confidence against him, which will now be put to the party's membership at the upcoming EGM.
UKIP's finances are also known to be in poor health, hastening Towler's departure.
He said in a statement that he would be "consciously uncoupling from UKIP" and commented: "13 years? Really? Well that was a blast."
New venture for ex-journo
Towler is setting up a reputation management consultancy, provisionally named CWC, which stands for "crisis, what crisis?". He told PRWeek he already had two clients "not in politics", but declined to give details. He will remain a UKIP member.
Prior to UKIP, he edited now defunct Brussels satirical magazine The Sprout, claiming that this made him one of the "most hated men in Brussels".
Towler has been a stable presence through a series of changes in the party's leadership, and the shortlived appointments of two high-profile journalists in a comms director role in 2013 and 2014.
Although he has been involved in controversies, he is also well-liked in Westminster and by journalists - being referred to as "a delight" by Michael Crick in 2016; the Channel 4 journalist also told PRWeek that UKIP's press team made it "probably the easiest party around to deal with".
UKIP also lost another respected, albeit more junior, PR operator in the summer when John Gill moved to City-focused agency Greentarget.
- Click to read Towler's profile in PRWeek's 2017 Power Book