Born and brought up in Aberdeen, Scotland, Rachel Cowie married William Milne of the London Missionary Society (LMS). After he finished missionary training and was ordained in 1812, they departed for China, where he was the second Protestant missionary to arrive. The Milnes had intended to settle in Macao as an alternative to Canton, where the Ch'ing government prohibited missionary activity. However, after being evicted from Macao, in 1815 they settled in Malacca, where the LMS mission established the Anglo-Chinese College, of which William Milne became the first principal.
Rachel Milne's duties, as outlined by her husband, were to nurture her spiritual life, look after and educate their children, learn the Chinese language, take care of her health, and prepare herself to assist the missionary work. But, unable to tolerate the tropical climate and frequently ill, she died in 1819, leaving three children. She was the first China missionary wife to die in the mission field. She was buried in the Dutch cemetery in Malacca. Her son, William Charles Milne, later became a missionary of the LMS in China.