Clarke married Marilyn Mayfield, an American divorcee with a young son. The marriage was short-lived.

Clarke and Marilyn Mayfield divorced. While Clarke generally kept his personal life private, the divorce was a significant event in his life. The reason for the divorce was irreconcilable differences.

Clarke maintained a close friendship with Leslie Ekanayake, a Sri Lankan man who became his long-time caregiver and assistant. This friendship was a vital part of Clarke's life in Sri Lanka, providing companionship and support. The exact nature of the relationship was subject to some speculation.

Throughout his life, Clarke maintained a very private life. He never remarried, and there was much speculation about his sexuality. In the early 1990s, an article in a magazine led to controversy when the writer suggested that he and Ekanayake had a more than platonic relationship.