Amber Leeanne DuBois, 14, was last seen February 13 walking to Escondido High School. There have been few leads for detectives, and a headquarters for weekend searches recently closed.
Since she disappeared, "I have felt like my heart has been ripped out of my body,'' Maurice DuBois wrote. "Words can't explain how I feel every day without you here.''
Maurice wrote that he couldn't imagine Father's Day being worse than when Amber's grandfather died, but "this year is by far worse. I don't have my Amber here.
"It has been 128 days that our family has been torn apart, and each one seems longer than the last. There is no day that goes by that I don't cry for hours before falling asleep.''
Maurice DuBois closed the letter by saying thousands of people were praying for her, and he had faith that she would return safely.
Officials with the Escondido Police Department were not immediately available to comment on the status of the investigation.
Detectives previously expressed interest in locating a large burgandy pickup truck that might be connected with a pair of molestations of young girls in San Diego.
The Escondido Police Department in April released surveillance video that showed such a vehicle pulling into the bus maintenance yard at Amber's school for three minutes on the morning she disappeared.
Last month, it was reported that a similar pickup truck was driven by a suspect possibly connected to the San Diego molestations.
The victims, ages 5 and 6, were separately assaulted on April 1 at the College Grove Wal-Mart store, and May 17 at a Wal-Mart in Kearny Mesa.
Surveillance cameras at both stores showed a 6-foot tall white man entering a four-door burgandy pickup truck with a chrome box in the bed, police said.
No arrest has been made in the molestations.
Amber is 5 feet 5 inches tall and 130 pounds, with short brown hair and blue eyes. Her parents said she had no history of running away from home.
There is a $50,000 reward for Amber's safe return. A Web site about Amber is at www.bringamberhome.com.