The 44-year-old has been a player and manager with the Trawlerboys for more than 20 years and will be staying on as director of football in a consultancy basis at the Southern League Premier Division Central side.
A spokesman for the Lowestoft board of directors spoke on the move and how gutted the club are that such an iconic figure has moved on.
“While we are all gutted to be losing Jamie, this was too good an opportunity for him to miss.
“However, Godders will still be involved in his head of football role with the club, and on the board of directors, as he will still be the lead on all football development matters from the first team down to our thriving youth section - so his DNA will still be prominent within the club.”
Former Lowestoft keeper and assistant manager Andy Reynolds has been appointed as the club's new first team manager but not before taking charge of the club for one last home match against Harborough Town this Saturday.