Sweden granted citizenship last week to Ahmadreza Djalali, a Stockholm-based specialist in emergency medicine.
He was arrested during a brief visit to Iran in April 2016 and found guilty in October of passing information about two Iranian nuclear scientists to Israel's Mossad intelligence agency that led to their assassinations.
Iranian foreign ministry spokesman Bahram Ghasemi said the decision to grant a convict citizenship was “very strange, unprincipled and questionable” and that the Swedish ambassador was summoned on Monday.
“Iran's strong protest was conveyed to the Swedish ambassador with regards to the move by the Swedish government to grant nationality to a person who has confessed to spying for Mossad and the Zionist regime and participating in killing Iranian scientists,” Ghasemi said in a statement on the ministry website.
Ghasemi emphasised that Iran does not recognise dual nationality, and that Djalili will be treated purely as an Iranian citizen.
The Supreme Court confirmed Djalali's death sentence in December, which was criticised by human rights group Amnesty International as running “roughshod over the rule of law”.
Djalali has claimed he is being punished for refusing to spy for Iran while working in Europe.
His lawyers say they were blocked from presenting submissions ahead of the Supreme Court hearing.
The sentence has been condemned by the Vrije Universiteit Brussel in Belgium where he was a visiting professor. The European Union has said it is closely following the case.
A total of five Iranian scientists — four of them involved in the country's nuclear programme — were killed in bomb and gun attacks in Tehran between 2010 and 2012 at the height of tensions over the country's nuclear ambitions.
Iran has accused Mossad and the CIA of ordering the killings.