Born in Wake County, North Carolina, Yates and his wife, Eliza Moring Yates (1821-1894), were the first missionaries appointed from their state and among the earliest Southern Baptist missionaries to China. Although he grew up in a very poor home, he was blessed with parents who were devout Christians and who shaped their son's life accordingly. Converted at the age of 17, Yates soon sensed a call to ministry. In order to secure an education he worked his way through Wake Forest Academy and College from which he received a B.A. in 1846.
Appointed as a missionary to China by the Southern Baptist Convention Foreign Mission Board (SBCFMB) in August of that year, Yates married in September and was ordained in October. One year later the couple arrived in Shanghai, the most northern of the recently opened treaty ports, and they labored there for 42 years. Working under extremely adverse conditions, Yates learned the language, endured the Chinese xenophobia, survived the Taiping Rebellion, overcame loneliness and severe illness, adapted to the culture, and enjoyed a productive ministry. He organized churches, built houses of worship, established schools, and laid the foundation for what came to be known as the Central China Mission of the Southern Baptist Convention Foreign Mission Board.
Intermittently, he was required to support himself and his family by working as an interpreter, a teacher of Chinese to English businessmen, a municipal employee, and U.S. vice-consul in Shanghai. He was offered several diplomatic posts, including that of consul-general, and was also invited to become president of Wake Forest College, but declined all these opportunities in favor of his missionary work. His publications included First Lessons in Chinese, for learning the language, and a colloquial Chinese translation of the New Testament. By his work and his shrewd investments, Yates bequeathed a number of legacies to Christian causes. Both Yates and his wife died in China and are buried in Shanghai.