The Grade 2 listed building said to be one of the finest mid Victorial churches in Wales is in the middle of a £200,000 restoration project.
The Heritage Lottery Fund has already helped towards th cost of major external work and will now stump up another £44,000 towards the second phase of the project.
This will entail essential stonework repairs, repointing, repair and releading of clerestory windows and will cost £90,000. Work will start at the end of April and take 14 weeks to complete.
The Vicar of Rhyl, Canon John Glover was delighted with the news and said: "This is wonderful news for the Parish and indeed the whole town, who use and rely on St Thomas' for so many events and activities over and above its importance as a place of worship for nearly 150 years.
"We are hugely grateful to the Heritage Lottery Fund for their continuing generous support, without which this work would simply be far beyond our means. I am sure the lottery players who have made this possible will understand our deep appreciation.
"It will finalise the vital restoration of the outside of this important building which has been ravaged by sea air and in urgent need of attention."
Canon Glover said he was expecting to receive additional funding from Cadw, the Welsh Monuments body, towards the overall cost.
"This will still mean we shall have to find at least £15,000 from within the Parish as our contribution but I am confident that local people will get behind us to ensure that St Thomas's continues to play a key role in the life of Rhyl and district."
Built in 1861, St Thomas', with a seating capacity of 1020 beneath a bell tower and spire rising to 203 feet, one foot higher than the Marble Church, Bodelwyddan, stands in a conservation area and has been recognised by the HLF as a focal point for the town and an important meeting place for the whole community.
Its eminent architect, Sir George Gilbert Scott, famed for building the Albert Memorial and the Foreign Office, described St Thomas' as one of the finest mid-Victorian churches in Wales.