The vigil, being held at Farm Street Church in Mayfair, comes amid renewed hopes for the safety of Fr Paolo Dall'Oglio who was kidnapped in July 2013.
The Italian Jesuit had served for more than three decades at a monastery outside of Damascus.
He had been expelled from Syria in 2012 after criticising the Assad regime but was smuggled into rebel held territory in 2013. He was kidnapped whilst out walking in Raqqa.
Early reports from sources inside Raqqa suggested that the priest had been executed by the extremists but an IS defector later said that he had seen Fr Paolo alive in a prison in 2015.
The Novena for Syria, which will be held until 7 April, will be a time of "of prayer and reflection... a spiritual vigil that will revitalise our faith that Father Paolo will be returned home safely to us," according to organiser Fr Dominic Robinson.
The nine days of prayers will mark the third anniversary of the death of Fr Frans van der Lugt, another Jesuit priest who was shot dead while working in Syria. He had stayed in the besieged city of Homs to help people who were trapped there.