Kurdish fighters, who have provided protection for Christians there, are being targeted by Turkey in an attempt to create what it calls a 'safe zone'.
Open Doors says there is growing concern the ongoing conflict will leave Syrian Christians vulnerable to attack by members of Islamic state, without Kurdish defence.
Speaking to Premier, Open Doors CEO Henrietta Blyth, said: "There is a very real fear of Islamic State members being freed from prison and starting the persecution of Christians and others again, as a result."
The Syrian border town of Qamishli, which has a strong Christian presence, has experienced a number of bombings and missile strikes as a result of the fighting.
Christians are concerned that the IS members held in the local prison could escape if it is hit.
Blyth says that Christians are expected to flee the region again, "as a result of the aerial bombardment", following reports from local pastors.
Hundreds of thousands of Christians have previously been displaced as a result of the Syrian Civil War which began in 2011.
Open Doors say they know of at least 90 Christian families who have fled Qamishli this week.
In response to this the charity has launched a new campaign to provide financial support to churches and families impacted by the bombings and to encourage people to stay and allow "the light of the gospel to continue to shine in these areas."
Open Doors are calling on the international community to put pressure on the Turkish government to agree to a ceasefire and have encouraged Christians everywhere to pray for the situation.
Blyth said: "Pray that politicians and military leaders show compassion on civilians, pray that imprisoned IS members continue to be contained and not released and pray that those who've been injured will be able to find the right treatment."