Thomas O'Neill died on 13 March 1890 at Fairmount aged 59. His funeral service was held in St Mary's Cathedral, and he was buried in Waverley cemetery. He was said to have been a most amiable man, held in high regard by all that knew him. His was deeply involved in not only Irish and Catholic affairs, but public affairs in general. His charity spanned many years with his support of St Vincent's Hospital, The Good Samaritan Refuge and The Benevolent Asylum being on-going. His purse was never closed to charity. His final act before his illness was to donate the land and money to help the establishment of the Catholic church and school at Rydalmere.