"Some may remember that I intended to retire in 2016, but with the resignation of Prime Minister Rt Hon Sir John Key, I was convinced to remain in the role to help ensure a stable transition of leadership to Rt Hon Sir Bill English and to deliver our 2017 General Election campaign," he said.
National leader Christopher Luxon thanked Goodfellow for his service to the party.
"Peter has made an immense contribution to the National Party, and on behalf of the parliamentary caucus I have thanked him for his more than 13 years of stellar service as president.
"I have found Peter's experience, knowledge and wise counsel invaluable in the time that I have been Leader.
"Peter now feels it is a good time to stand down as president given the party's renewal has been completed with a new leadership team established, the caucus unified, and a refreshed team of political and campaign staff in place," Luxon said.
Goodfellow's tenure as leader was marred by some controversy, and he copped criticism in 2020 and 2021 for the party's flawed candidate selection and outmoded backroom operation.
Former Speaker David Carter was elected to the board and challenged Goodfellow for the presidency in 2021.
Carter failed in that attempt and resigned from the board shortly after, saying he had no confidence in Goodfellow.
"I haven't enjoyed my nine months on the board and I have no confidence in Mr Goodfellow as chair of that board. Therefore it would have been inappropriate for me to remain," Carter said at the time.
"The review we did after the election raised two significant points: the governance of the party from board was dysfunctional, and second, we did not have enough money in our coffers to campaign.
"I don't think either of those things will change while Mr Goodfellow is president."