Yap is married to ABS-CBN personality and Purefoods endorser Kris Aquino, the daughter of slain former senator Benigno Aquino, Jr. and former President Corazon Aquino. Yap and Aquino's relationship was rumored as early as 2005 before they acknowledged this on various interviews. In various interviews in 2006, both admitted to have tied the knot as early as mid-2005, and kept the marriage unknown to the public. The couple is expecting to have a baby on June 2007.
Even before the marriage there were news that James Yap have a child to another woman.James Yap is now the talk of controversy after news circulated that he had an affair with a facial attendant at the Belo Medical Group named Hope Centeno.This eventually led to Kris asking for "space" with the star cager.