Franchione and his wife, the former Kim Kraus, began dating after he took her on a tour of his alma mater, Pittsburg State University, at the request of her father. They married shortly after, in 1977. The couple have two daughters, Elizabeth Ann and Ashley Renee. Franchione also has a son, Brad, who is the head football coach at Blinn College, from a previous marriage. The Franchione family runs Coach Fran Charities, which raises money for children with special needs.
After graduating from Pittsburg State, Franchione served as the head football coach at several high schools in Missouri and Kansas. In 1978, Franchione was hired to be an assistant coach at Kansas State University, a position he would hold until he was hired to be the head coach at Southwestern College in Winfield, Kansas in 1981. During his two years at Southwestern, he led the team to a 14-4-2 record.
After two seasons as offensive coordinator at Tennessee Tech in 1983 and 1984, Franchione was hired as the head coach for his alma mater, Pittsburg State. He stayed on as head coach through 1989. During his time with the Gorillas, he led the team to a 53-6-0 record and was named NAIA Coach of the Year in 1986 and 1987. At Southwest Texas State University (now Texas State University-San Marcos) from 1990 to 1991, he led the team to a 13-9-0 record.
In 1992, Franchione took his first head coaching job in Division 1-A the University of New Mexico. In his six seasons in New Mexico, he led the Lobos to a 33-36 record, including a 9-4 mark in 1997. That year, the Lobos were the WAC Mountain Division champions and received an invitation to play in the Insight.com Bowl, their first bowl berth since 1961.
In 1998, he became the head coach at TCU and promptly turned their fortunes around, going from 1-10 the year before to 7-5 and a berth in the Sun Bowl, where they defeated USC and set the record for least rushing yards allowed in a bowl game. In 1999, he again led the Horned Frogs to a bowl game on the wings of junior tailback LaDainian Tomlinson, who led the nation in rushing. There was much momentum going into the 2000 season, as LT was hyped as a Heisman Trophy candidate and the Frogs were being touted as a possible BCS contender before a disappointing loss to San Jose State. Despite the loss, the Frogs finished the season 10-1 and were co-champions of the Western Athletic Conference and accepted a bid to the Mobile Alabama Bowl. Before the bowl game, Franchione accepted the job at Alabama, and current TCU coach Gary Patterson coached them in the bowl game instead.
In 2001, Franchione became the head coach at the University of Alabama and led the team, who had posted a 3-8 record the prior season, to a 7-5 record in 2001 and a 10-3 record in 2002. Following Alabama's victory over the University of Hawaii and the firing of R.C. Slocum, Franchione resigned at Alabama and was named head coach at Texas A&M University after publicly stating that he would not leave.
Upon being hired by Texas A&M, Franchione brought his entire coaching staff to College Station with him for the 2003 season, in which the Aggies finished 4-8. Franchione began the rebuilding process in 2004 as the team improved to 7-5, 5-3 in conference, including an overtime victory over Texas Tech, and advanced to the Cotton Bowl. Because of his team's improvement, Franchione was a finalist for the BCPC Association's Coach of the Year Award. Franchione's Aggies regressed to a 5-6 season in 2005 which prompted him to dismiss defensive coordinator Carl Torbush. Torbush was replaced by former Western Michigan head coach Gary Darnell. In 2006, The Aggies again rebounded under Franchione, posting a 9-4 record that included Franchione's first win over arch-rival Texas. After the season, the Aggies faced #20 California in the Holiday Bowl, a game the Aggies lost 45-10. Franchione is posting an overall record of 25-23 at College Station, including 2-10 against the Aggies' significant rivals Oklahoma, Texas, and Texas Tech.