His first positions were as curate of Denio and Llanor near Pwllheli, Gwynedd (1853) and chaplain of Tremadog near Porthmadog (1854–1855).
He then became perpetual curate of Penmachno before his appointment as vicar of Mynydd Llandegai, near Bangor in 1860, where he remained for 34 years.
He published in English and in Welsh, including a collection of sermons on the miracles of Jesus.
Thomas was an editor on the monthly Welsh language periodical Amddiffynydd yr Eglwys.
[1] He married Anna Thomas, who became active in attempts to reform the National Eisteddfod in the 1870s and 1880s, and who was nearly appointed as a professor of modern languages at the University College of North Wales, Bangor.