In 2007, it was revealed by Lorna Tolentino on "Startalk" that her husband had been diagnosed with periampullary cancer. Fernandez underwent treatment in Tokyo, Japan. After a healing Mass on May 10, 2008 by several friends at the Christ the King Church, Quezon City, he was rushed to a San Juan City hospital for back pains. The "Sun Star" reported that Fernandez was actually suffering from pancreatic cancer, instead. Fernandez celebrated his 25th wedding anniversary with Lorna Tolentino on June 1, 2008. He suffered a seizure three days later on June 4, but refused to be taken back to the Cardinal Santos Memorial Center in San Juan City. Fernandez died from periampullary cancer at his home in Quezon City on the morning of June 7, 2008.