Parkinson has dealt with significant disruption since coming into the position with notably the closure of the grandstands at Yarrow Stadium being one of a number of hurdles faced under his tenure.
TRFU chairman Lindsay Thomson said it is disappointing to lose Parkinson.
"He will be missed. He has carried a heavy load in the most difficult of circumstances facing the Union. He certainly received a hospital pass when the Yarrow Stadium grandstands were also closed, but he has worked extremely hard to ensure our offering for the 2019 season, and the business, is in as good shape as possible.
"Jeremy has met the challenges head on and connected very well in the community."
Across a tumultuous 19 months Parkinson was responsible for navigating the province with the relocation of the TRFU to their temporary premises in the Tuson Stand at the Pukekura Raceway. In a challenging 2018, there still were some notable positives especially in the community game where Taranaki Rugby grew the game to exceed 7000 registered rugby players for the first time.
Parkinson said 2018 was the worse year in Taranaki rugby history.
"Although I will be remembered as the CEO who presided over 2018, which will go down as the worse year in our very proud history, the game is in very strong heart in the province with year on year participation growth and very loyal and parochial clubs that support rugby. In this region rugby is ingrained into our society, it is what you do on a Saturday".
Parkinson also acknowledged the very strong commercial support from key businesses in the region.
"The Yarrow family are huge contributors to Taranaki Rugby and the wider community with their generosity. I personally want to thank John and Rosaleen Yarrow and their son Philip as our principal partner.
"Yarrows the Bakers are fantastic supporters and understand what rugby means to this community and that when the Bulls play well it galvanises support from everyone within the district. Our strong commercial database of support is critical to our survival and I want to thank each and every business that is associated with Taranaki Rugby".
"I will miss the people, I will miss my great staff and also everyone who gives their time to see the game flourish in every rugby club throughout the region.
"This is a people business. I am proud to say that I have visited every rugby club in the region over the last 19-months. It's all about people and thanking them for what they do in their communities to keep our game alive and healthy".
"The opportunity that we have taken through all the adversity that we faced last year was that we have had to re-connect with our community and getting around consulting on our new strategic plan has been healthy for the future of the game and the Union."
The process to replace Parkinson will start immediately. Lindsay Thomson says the board are meeting this week to discuss the options.
"We must ensure that we appoint the right person to take the business forward from the rebuild foundations that Jeremy has laid".
Parkinson wanted to acknowledge the support of his wife Julie, daughter Ellamae and son Monty as they followed him to New Plymouth to take this role.