Christian Solidarity Worlwdie says intelligence agents entered the homes of Yasser Mosayebzadeh, Saheb Fadaie and Mehdi Reza Omidi (Youhan) in Rasht earlier this week.
After being ordered to report to a station to answer questions they were later told to leave the country.
CSW says the reason for the raids remain unclear; however, Mehdi Reza Omidi (Youhan) was part of a group of four Christians who in October 2013 were charged with drinking alcohol during a communion service, and possessing a receiver and satellite antenna. The group was sentenced to 80 lashes each for the offences.
The three men are also leaders of the church run by Pastor Yousef Nadarkhani, who was sentenced to death for apostasy in 2010 and acquitted in 2012.
Speaking about the raids, CSW's Chief Executive, Mervyn Thomas said: "CSW is concerned by Monday evening's raids by the Iranian authorities, who continue to harass the Christian community without cause.
"We applaud the fact that following the murders of 21 Egyptian Christians in Libya, the Twitter account of Ayatollah Khamenei highlighted that Islam advocates "fairness and justice towards the followers of other religions", and used the hashtag #ChristianLivesMatter.
"We therefore call on the Supreme Leader to ensure that his country's religious minorities experience fairness and justice, and that the authorities illustrate by their actions that the lives of Iranian Christians also matter."