Thomas Francis Lillis (March 3, 1861 – December 29, 1938) was an American prelate of the Roman Catholic Church. He served as Bishop of Leavenworth, Kansas (1905–1910) and Bishop of Kansas City, Missouri (1913–1938).
One of eleven children, Thomas Lillis was born in Lexington, Missouri, to James and Margaret (née Jordan) Lillis. His parents were both Irish immigrants; his mother was born in County Cork while his father was from County Clare and worked as a railroad contractor and later police commissioner of Kansas City under Governor Meredith Marmaduke. He attended public schools in Lafayette County before studying at Niagara University in New York, from where he obtained a Bachelor of Arts degree. He completed his theological studies at St. Benedict College in Atchison, Kansas.
At age 24, Lillis was ordained to the priesthood by Bishop John Joseph Hogan on August 15, 1885. He then served as a curate in Shackleford until 1887, when he became pastor of Westport. He was rector of St. Patrick's Church in Kansas City from 1888 to 1904. He also served as vicar general of the Diocese of Kansas City.