The International Committee of the Red Cross posted a photograph on its Twitter account of the girls lining up to get into a helicopter.
The ICRC said it on Twitter that it "acted as a neutral intermediary to facilitate" the girls' transport back home.
WATCH: Released Chibok Girls at Medical Center
The girls are expected to meet with President Muhammadu Buhari later in the day.
The group of girls, released Saturday, had been kidnapped in 2014 in the town of Chibok near Nigeria's borders with Chad and Niger.
Nigerian government officials confirmed the releases early Sunday.
The girls gained their freedom following protracted negotiations between Boko Haram and government envoys.
A statement from President Buhari's office says the girls were released "in exchange for some Boko Haram suspects held by the authorities."
According to the statement, Buhari is optimistic about the release of the remaining girls seized in the Chibok raid.
The president expressed his appreciation in the statement to the Nigerian security agencies and the military for their roles in the release of the girls. He also thanked the government of Switzerland, the International Committee of the Red Cross, and local and international NGOs.
Kidnapping sparked international uproar
Authorities say 276 girls were kidnapped from a government-run girls' secondary school in Chibok on April 14, 2014. Nearly 60 girls who escaped during the first hours said their abductors forced them from dormitories into trucks that headed into the bush.
Days later, a widely distributed video purported to show about 100 of the missing girls. Boko Haram claimed the captives had converted to Islam, and said they would only be released in exchange for militants held by the Nigerian government.
At the time, Boko Haram leader Abubakar Shekau vowed to sell the girls as slave brides.
The abductions triggered an international outcry, including condemnation from the U.N. Security Council. U.S. first lady Michelle Obama co-launched a media campaign to gain the girls' release.
First girls released last year
There was no sign of the Chibok schoolgirls for more than two years, until one girl -- by then a mother with a young infant -- turned up last May. Two other girls made their way to government-controlled areas later in the year, and a group of 21 captives was released in October.
Nigerian Defense Minister Manir Dan Ali, however, told VOA's Hausa service last month it might take years to find all of the Chibok girls. He spoke as grieving families marked the third anniversary of the girls' disappearance, and as government troops searched known Boko Haram hideouts in the Sambisa forest -- a vast area extending into three states in Nigeria's northeast.
Boko Haram, whose declared aim is to create an Islamic state, has killed thousands of people and displaced more than 2 million during its insurgency, now in its eighth year.
Boko Haram's other victims
U.N. officials have stressed that the Chibok girls are not Boko Haram's only victims.
The militants have seized at least 2,000 other girls and boys since 2014. Many of those captives were used as cooks, sex slaves, fighters and even suicide bombers, according to Amnesty International.
Boko Haram has increased its use of children as suicide bombers in the Lake Chad region, where 27 such attacks were recorded during the first three months of this year, three times as many as during the same period in 2016, according to U.N. children's agency UNICEF.