Pastor Behnam Irani who is already serving a jail term will now spend a total of 12 years in prison.
He was initially arrested in December 2006 and sentenced in 2011 to six years imprisonment for "action against the state" and "action against the order".
Pastor Matthias Haghnejad and deacon Silas Rabbani, who previously had capital charges against them dropped, were also jailed.
All three men are being transferred to prisons in the north of the country, which have extremely hot climates. The prisons they will be held in are hundreds of miles away from their family homes.
The sentences are seen as an indication of the surge in repression under the Rouhani presidency targeting religious and ethnic minorities.
This has occurred despite his earlier promise to uphold the rights of religious minorities during the run-up to elections last year.
Christian Solidarity Worldwide's chief operating officer Andy Dipper said: "We are deeply concerned by the six-year sentences given to pastors Irani and Haghnejad, and deacon Silas Rabbani, and the fact that they will serve these sentences so far from their families and hometowns.
"We are particularly appalled by the extra six years given to pastor Irani, who has already endured ill-treatment whilst in prison and now faces nearly a decade in prison on trumped-up charges.
"We urge the Iranian government to release without delay every person who is imprisoned for their faith.
"Their incarceration contravenes international covenants guaranteeing freedom of religion or belief, to which Iran is party."