The Church of Iran leader wanted to take action after hearing his 15 year old son Yoel had been told he could not return to school as he had not completed Islamic studies. Religious minorities are normally exempt from this class.
His 17 year old son Daniel has also been denied a school report card which is needed to enroll onto a higher education course.
They're being targeted because authorities say children of Christian converts should be treated as Muslims.
Nadarkhani says this shouldn't apply because he never practiced Islam prior to his conversion.
He said his hunger strike is for his own children but also other Christian youngsters who are targeted.
It's unknown what impact the strike had on authorities but his health is said to have deteriorated.
Religious freedom charity Christian Solidarity Worldwide (CSW) has been campaigning on his behalf.
Chief executive Mervyn Thomas said: "CSW continues to call for an end to the practice of denying access to education on account of a child's religious beliefs, as has been the case for Pastor Nadarkhani's sons. Children should not be penalised because of their faith or that of their parents.
"Moreover, Pastor Nadarkhani himself should not be in prison for having adopted a religion or belief of his choice in accordance with the International Covenant on Civil and Political Rights, to which Iran is party.
"We reiterate our call for his release, and that of others from religious minority communities who are currently imprisoned on account of their faith."
Nadarkhani is serving a ten-year prison sentence in Evin prison in Tehran after being accused of crimes against the state linked to the running of churches.
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