In 1842, Anderson married Hannah Longherst from Aberdeen, an assistant with his show. The following year their son John Henry Jr. was born. In 1845, Anderson's mistress Miss Prentice gave birth to Philip Prentice Anderson, but died in childbirth. Anderson, however, supported the child for his entire life. Anderson would also have two daughters – Helen and Alice – who assisted in their father's show and later became successful magicians, and a second illegitimate son with a member of his touring troupe.