Thomas Kirk was born in Coventry, Warwickshire, England, on 18 January 1828, the son of George Kirk, a nurseryman, and his wife, Sarah West, a nurserywoman and florist. He showed a keen interest in botany from an early age and worked for a time as a nurseryman. Later, he worked at Newarks' timber mill in Coventry. On Christmas Day 1850, at Coventry, he married Sarah Jane Mattocks, a silk marker. In 1862 poor health and economic pressures led him to emigrate to New Zealand. With his wife and four children he sailed from London on the Gertrude, arriving in Auckland on 9 February 1863.
Botany quickly became Thomas Kirk's dominant interest. He began collecting within a month of his arrival and prepared a collection of ferns and other plants for the New Zealand Exhibition in Dunedin in January 1865. He worked as a surveyor in 1866, and in May 1868 was appointed meteorological observer for Auckland. A month later he became secretary of the Auckland Institute and curator of its museum, a post he held for the next five years.
While in Auckland Kirk travelled widely on botanical expeditions, writing and publishing papers on his discoveries. He visited Great Barrier and Little Barrier islands in 1867, the east coast of Northland in 1868, the Thames goldfields in 1869, the Waikato district in 1870, and Rotorua and Taupo in 1872. He served from 1869 to 1873 as secretary and treasurer of the Auckland Acclimatisation Society, taught botany at the Auckland College and Grammar School and in 1871 was elected a fellow of the Linnean Society of London.
Thomas Kirk moved to Wellington in early 1874 and from then until 1880 lectured in the natural sciences at Wellington College, at that time affiliated to the University of New Zealand. Kirk proved an excellent teacher, popular with both staff and students. He joined the Wellington Philosophical Society in July 1874, becoming president from 1878 to 1879, and served several terms as a governor of the New Zealand Institute. In 1879 a royal commission advocated the separation of university and secondary education. Although Kirk's appointment was terminated because he represented university interests, the college raised funds to retain him for another year.
In 1881 Thomas Kirk became a lecturer in natural science at Lincoln School of Agriculture, Canterbury; he remained there until 1882, and returned for short periods in 1883 and 1884. For Kirk it was a frustrating period: he could not find suitable housing and his health was poor. Nevertheless, he collected plants in Arthur's Pass, Banks Peninsula, Lake Wakatipu and Stewart Island.
At the end of 1884 the government engaged him to report on the country's indigenous forests and in December 1885 he was appointed chief conservator of forests. He formed the forest and agriculture branch of the Crown Lands Department, drew up regulations to reduce the wasteful misuse of forests, and by 1888 had organised the allocation of 800,000 acres as forest reserves. A change of government and economic recession in 1887 forced retrenchment. Kirk was made redundant but was retained for three months to complete his most significant publication, Forest flora of New Zealand (1889).
For the remainder of his life Kirk continued his botanical interests. In 1890 he visited the Snares, Auckland, Campbell and Antipodes islands and Stewart Island; four years later he explored the headwaters of the Turakina and Rangitikei rivers.
Kirk was a kindly, gracious man with firm Christian convictions. He was a foundation member of the Wellington Baptist Church, serving as secretary and deacon for many years. He was elected president of the Baptist Union of New Zealand in 1892. His quiet humour and likeable, though reserved, personality endeared him to family and friends. For over 30 years he kept up a widespread correspondence with students and fellow botanists in New Zealand and overseas. He contributed over 130 papers to the Transactions and Proceedings of the New Zealand Institute and several other journals. His most important published works, other than Forest flora, were his Report on the durability of New Zealand timbers (1875), and Students' flora of New Zealand, published posthumously in 1899.
Thomas Kirk died in impoverished circumstances at Plimmerton on 8 March 1898 and was buried in an unmarked grave in Karori cemetery, Wellington, survived by his wife, Sarah, and five of his nine children, including Lily, a well-known suffragist and temperance campaigner. For more than three decades he had been the leader of botanical inquiry in New Zealand.