It is an active Anglican parish church in the Deanery of Kendal, the Archdeaconry of Westmorland and Furness, and the Diocese of Carlisle.

The Paley and Austin building replaced an earlier church of 1773, and cost about £3,000 (equivalent to £360,000 in 2023).

In 1885, composer Mary Augusta Wakefield and her sister Agnes organized a music festival to raise money for St. Thomas'.

The church was provided with an organ by Wilkinson of Kendal which was rebuilt in the 1980s by the East Anglian firm Holmes & Swift.

Its benefice was united with that of St Patrick, Preston Patrick,[6] although the latter parish is now served by the Kirkby Lonsdale team ministry, whereas Crosscrake is in a group of parishes in the Kendal area (the Helm group).