The PM told president Hassan Rouhani Ms Zaghari-Ratcliffe's confinement in the country is "completely unacceptable" as he urged him to allow her a safe return to the UK.
Ms Zaghari-Ratcliffe had her ankle tag tag removed on Sunday, following the end of her five year prison sentence, but she must attend court again this Sunday to face a second set of charges.
Mr Johnson said that while the removal of Ms Zaghari-Ratcliffe’s ankle monitor was welcome, her continued confinement remains completely unacceptable and she must be allowed to return to her family in the UK," according to a Number 10 readout of the call.
Upon her release, her husband Richard Ratcliffe said that “it’s a mixed day for us” and “Nazanin is genuinely happy” to be free of her electronic bracelet.
He said: “I’m a bit more guarded. It feels to me like they have made one blockage just as they have removed another, and we very clearly remain in the middle of this government game of chess.”
Mr Ratcliffe added: “She is having a nice afternoon, has turned her phone off and is not thinking about the rest of it.
“But she remains in harm’s way, even if today she is determined not to feel it.”
The 42-year-old’s family had been waiting to hear news of her fate as Sunday marked the end of her sentence.
She was jailed in Iran after being accused of plotting to overthrow its government – charges which she vehemently denies.
Mrs Zaghari-Ratcliffe, of north London, was arrested at Tehran’s Imam Khomeini Airport while taking her young daughter Gabriella to see her parents in April 2016.
Human rights groups say the charity worker, who was employed by the Thomson Reuters Foundation at the time of her arrest, was jailed with no evidence and her trial was unfair.
Also during the call the PM "stressed that while the UK remains committed to making the Iran nuclear deal a success, Iran must stop all its nuclear activity that breaches the terms of the JCPoA and come back into compliance.
"He stressed the importance of Iran seizing the opportunity presented by the United States’ willingness to return to the deal if Iran comes back into compliance. “The Prime Minister underlined the need for Iran to cease wider destabilising activity and be a positive force in the Gulf region.”
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