Gomes, who was arrested in January and accused of crossing into North Korea illegally from China, is the fourth US citizen in a year detained for allegedly sneaking into the communist country.
North Korean authorities sentenced Gomes in April to eight years of hard labour and fined him the equivalent of $700,000 for trespassing and committing a "hostile act".
The state-run Korean Central News Agency said Carter had apologised for Gomes' actions as part of the negotiations for his pardon.
The pardon "to set free the illegal entrant is a manifestation of [North Korea's] humanitarianism and peace-loving policy", the news agency said.
Gomes "admitted all the facts", state-run media said.
Jo Sung-rae, a South Korean human rights advocate who met with Gomes, said Gomes may have been emulating fellow activist Robert Park, who was detained after he crossed into North Korea a month earlier to highlight its human rights record.
Park was expelled a few weeks later.
US officials said Gomes had been teaching English in South Korea when he was caught.
Shortly before he left for North Korea, Gomes was photographed in the South Korean capital protesting Park's plight.
North Koreaand the US have no established diplomatic relations and Carter had arrived in Pyongyang on Wednesday on a private mercy mission, which his office and US officials stressed was not sponsored by the US government.
Though not an official visit, North Korea's state media said on Friday that Pyongyang, which has been sanctioned over its nuclear programme,had expressed its willingness through Carter to resume six-party nuclear disarmament talks, which have been stalled since April last year.
Similar expressions by the Northpreviously had attached onerous conditions to any resumption of talks that have been ruled out by both the US and South Korean governments.
The latest offer through Carter came just after a senior Chinese envoy on the nuclear dossier visited Pyongyang, as the North Korean leader was reportedly visiting China, its sole diplomatic and economic ally.
China's official Xinhua news agency said Carter spoke with North Korea's nuclear envoy Kim Kye-gwan for a few minutes before flying back to the US.
Carter also reportedly held dinner talks with the North's number two leader Kim Yong-Nam on Wednesday.
Al Jazeera's Steve Chao, reporting from neighbouring South Korea's capital, Seoul, said that the meeting was key because "Kim expressed North Korea's desire to denuclearise the Korean peninsula and also to resume the six-party talks".
"It was clear from the start, as soon as Jimmy Carter stepped down in Pyongyang, North Korea had a message to give. Carter was met on the tarmac on Wednesday by the North's nuclear envoy.
"The question now is how will the rest of the world react to this offer from North Korea and how legitimate or genuine is the offer."