The 78 students and three others were seized early on Sunday in the region's capital, Bamenda. A driver was also released, but the school's principal and a teacher are still being held.
The government has accused separatists in the English-speaking region of being behind the kidnapping. The Anglophone separatists have denied they were involved.
The secessionist movement took up arms last year to demand independence for the North-West and South-West regions - the two English-speaking regions in a country where French is the most widely spoken official language.
The kidnapped students, aged between 11-17 years old, are "frightened and traumatised but in good shape", Rev Fonki Samuel, Presbyterian Church Moderator in Cameroon, told the BBC Focus on Africa programme.
He said that they were being given food and being checked by the doctors before being released to their parents. He added that Bamenda's Presbyterian Secondary School - where they were seized - had been closed.
How were the children freed?
According to the Presbyterian Church of Cameroon, the students were abandoned in one of their buildings in the town of Bafut, about 24km (15 miles) from Bamenda.
"The release was done peacefully... by unidentified gunmen. They [students] were brought into the church premises," Rev Samuel said.
"The first information we got from them [kidnappers] is their call and they were telling us they intended to release the children yesterday [Tuesday] morning... but unfortunately it rained so heavily that could not happen.
"So [on] the evening of yesterday, surprisingly and by God's grace, the children were brought back to us."
The North-West and South-West regions are Cameroon's
two English-speaking regions
Rev Samuel told the BBC that 78 students, not 79 as earlier reported, had been released. He also revealed that Sunday's kidnapping was the second such case at the school in less than a week.
In the earlier 31 October incident, 11 boys were taken and then released. It is unclear who the kidnappers were but the church paid a ransom of $4,000 (£3,000) to secure their release, he said.
The army had been deployed to try and find the children taken on Sunday.
Who was behind the kidnap?
Rev Samuel told the BBC he was not concerned about who was behind the kidnapping, only "overwhelmed and happy" that the schoolchildren had been freed.
He said, "armed groups, gangsters and thieves" could be taking advantage of the insecurity in the region to kidnap people, and blame it on the government and separatists.
Cameroon's authorities have blamed the kidnap on Anglophone separatist militias - who have called for schools in English-speaking regions to be closed.
They want to create an independent state called Ambazonia.
Anxious parents had gathered on Tuesday at the Presbyterian Secondary School to try to get information about their children. A video of the hostages released on Monday showed one of the captives saying they had been seized by "Amba Boys" - the widely-used term to describe the separatist rebels.
Parents gathered at the Presbyterian Secondary School in Bamenda
after getting news their children had been kidnapped
An Anglophone group, the Ambazonia International Policy Commission (AIPC), has however denied that the separatists were behind the kidnapping, noting that the person recording the video appears to have a poor grasp of Pidgin-English, the language spoken widely in the Anglophone area of the country. One of the kidnappers was also apparently heard speaking French.
What is happening in English-speaking parts of Cameroon?
English-speakers in Cameroon have long complained that they face discrimination from Cameroon's Francophone majority.
They say that they are excluded from top civil service jobs and that government documents are often only published in French, even though English is also an official language.
Cameroon - still divided along colonial lines
Africa's borders were "carved up" by colonial powers
Colonised by Germany in 1884
British and French troops force Germans to leave in 1916
Cameroon is split three years later - 80% goes to the French and 20% to the British
French-run Cameroon becomes independent in 1960
Following a referendum, the (British) Southern Cameroons join Cameroon, while Northern Cameroons join English-speaking Nigeria