In 1989, Logan became an assistant coach at East Carolina University. He was the team's offensive coordinator under Bill Lewis from 1990–91, working alongside future Boston College Head Coach Jeff Jagodzinski. When Logan succeeded Lewis, Jagodzinski remained on staff for four years before accepting the offensive coordinator position at Boston College. The 1991 Pirate team finished 11–1, reached a top-10 national ranking and defeated NC State in the Peach Bowl. Logan served as the head coach of East Carolina from 1992–2002. He became the school's all-time winning coach, and led the Pirates to five bowl games, including the 1994 Liberty Bowl, the 1995 Liberty Bowl, the 1999 Mobile Alabama Bowl, the 2000 Galleryfurniture.com Bowl, and the 2001 GMAC Bowl. Logan's 1995 team finished with a 9–3 record and a No. 23 ranking in the final Associated Press poll. In 1996, ECU gave the Miami Hurricanes their worst defeat in the Orange Bowl in 12 seasons. In 1999, ECU upset #9 Miami at Carter–Finley Stadium in Raleigh, North Carolina, after Hurricane Floyd devastated Greenville. For this 9–3 season, which also included victories over West Virginia, South Carolina, and NC State en route to another bowl game. the team won the ESPNSpirit Award. He resigned on December 7, 2002 after a "substandard" 4–8 season. Three of Logan's quarterbacks; Jeff Blake, Marcus Crandell, and David Garrard went on to pro careers.
After a one-year hiatus from coaching, Logan entered the professional ranks in 2004 with the Berlin Thunder of NFL Europe, spending two seasons as the team's quarterbacks and wide receivers coach. During his first season, he helped head coach Rick Lantz lead the Thunder to a 9–1 regular season mark, tying the league record for wins in a season, and a 30–24 victory over the Frankfurt Galaxy in World Bowl XII. The following year, Berlin again finished the regular season in first place with a record of 7–3, but fell to the Amsterdam Admirals in World Bowl XIII, 27–21. In 2006, he served as the offensive coordinator and quarterbacks coach for the Rhein Fire. Logan helped Dave Ragone and Rohan Davey earn Offensive Player of the Year and All-NFL Europe honors.
Boston College
Logan rejoined former assistant Jeff Jagodzinski as offensive coordinator at Boston College in 2007. He helped develop quarterback Matt Ryan, who would win the ACC Player of the Year, the Johnny Unitas Golden Arm Award, the Manning Award and was named the AP NFL Rookie of the Year. In January 2009, Jagodzinski got fired after interviewing for the New York Jets head coaching vacancy. Logan was considered a candidate to replace him, and interviewed for the job with Boston College athletic director Gene DeFilippo. After the school had promoted defensive coordinator Frank Spaziani to the head coaching position, Logan decided to leave the program.
Logan was hired as the running backs coach for the NFL's Tampa Bay Buccaneers on February 11, 2009, reuniting him with Jagodzinski, the team's offensive coordinator. After Jagodzinski's firing in September 2009, Logan remained on the Buccaneers staff. After the Buccaneers 4-12 record in the 2011 season, Raheem Morris and his entire coaching were fired.
WRAL analyst
During 2013–2014 Logan worked as a special guest football analyst in a "cross divisional programming lineup" with multiple TV and Radio channels associated with WRAL-TV out of Raleigh, North Carolina. Logan would provide predictions and analysis focused specifically on college teams in the WRAL market and the Carolina Panthers of the NFL. WRAL-TV Sports Anchor, served as host of the TV segments. Logan would also be featured in front of a telestrator in a segment called "Coaching 101". In these segments he would explain the strategy behind common football plays, formations, and other elements of the game.
On January 28, 2015, it was reported Logan agreed to be the quarterbacks coach of the San Francisco 49ers. However, after just one season, he was relieved of his duties due to the firing of Jim Tomsula and hiring of Chip Kelly.
Birmingham Iron
In 2018, Logan became the offensive coordinator and quarterbacks coach for the Birmingham Iron of the Alliance of American Football.
Personal life
Logan and his wife, Laura, have two sons, Vince and Nate.