The bike-borne assailants today targeted the church in the Essa Nagri area of the city, Express Tribune reported.
Two people were killed in the attack, police said, adding the injured have been hospitalised.
After the attack, the community members with dead bodies staged a protest demonstration and blocked roads disrupting traffic, alleging government's "failure" to end attacks on Christians, according to the report.
Meanwhile, Balochistan Home Minister Mir Sarfaraz Bugti condemned the attack and expressed sorrow over the loss of lives.
The attack comes two weeks after four members of a Christian family were gunned down in Quetta a day after the community celebrated Easter on April 1.
In December last year, nine people were killed and over 40 injured in twin suicide bombings on another Church in Quetta.