Yousef Nadarkhani - who was acquitted of apostasy four years ago - was re-arrested in the country last week.
Pastor Nadarkhani was initially arrested and charged with apostasy in 2009, after going to his children's school to call the Muslim monopoly on Iranian education unconstitutional.
He was sentenced to death in 2010, a decision that was upheld by the Supreme Court in 2011.
The pastor repeatedly refused to renounce his faith during court hearings, in order to avoid the death penalty, and was released in September 2012, after his acquittal on apostasy charges.
Last week Pastor and Mrs Nadarkhani were arrested after VEVAK officers raided their home in Rasht.
The raid on the Nadarkhani home is reported to have been part of a series that targeted around ten Christian homes.
Three other Christians who were also arrested on 13 May are still in custody.
Christian Solidarity Worldwide's Chief Executive Mervyn Thomas said: "While CSW is relieved that Pastor and Mrs Nadarkhani have been freed, we remain deeply concerned for the welfare of Yasser Mossayebzadeh, Saheb Fadaie and Mohammadreza Omidi, who are still being held.
"The government must be held to account for its harassment of Iran's Christian community, in particular the constant raids on homes and repeated arrests which are without basis.
"We continue to call on Iran to fully respect its constitutional and international human rights obligations by ensuring that justice and equality before the law are guaranteed to all citizens, regardless of their religion or belief."