John Michael Hayden entered into collegiate coaching by joining the University of Louisville Mens Soccer program in 2012. The Cardinals won the Big East Conference tournament title and advanced to the NCAA elite eight in Hayden's single season with the Cardinals. Louisville had four players drafted into Major League Soccer including the number one overall draft pick, Andrew Farrell.
John Michael left Louisville to join Lipscomb University in 2013. While at Lipscomb Hayden helped the Bison to a program-best 12-4-1 record and Atlantic Sun Conference regular season title in 2014. The Bison were 21-13-4 overall during his two years in Nashville, racking up several conference honors in the process. Hayden helped coach the 2014 A-Sun Defender of the Year, Luke Gearin, and the A-Sun Freshman of the Year, Ivan Alvarado. Lipscomb received multiple votes in the NSCAA Top 25 and was ranked as high as No. 4 in the NSCAA Southeast Regional Poll during a landmark 2014 season.
In 2015 Hayden joined Xavier University as their Associate Head Coach. During his one season with the Muskateers the team compiled a 12-6-1 record. Xavier also earned an NSCAA national top 10 ranking while winning at both No. 2 Notre Dame and No. 1 Creighton. These results are widely considered to be the first time any team has knocked off the top two NSCAA-ranked teams on the road in the same season.
In 2016 Hayden returned to the University of Louisville.
Houston Dynamo selected Hayden in the first round (13th overall) in the 2007 MLS SuperDraft. He made his professional debut for them on 10 July 2007, in the Lamar Hunt U.S. Open Cup against Charleston Battery. He was loaned out to USL-1 side Cleveland City Stars in May 2009. While at Cleveland he landed USL-1 team of the week accolades following performances against the Portland Timbers and the Minnesota Thunder.
On July 1, 2009, Hayden made his first start of the 2009 season against the Austin Aztex of the USL First Division in the third round of the 2009 Lamar Hunt U.S. Open Cup, a game which Dynamo won 2-0. Hayden played in subsequent cup games for Dynamo against Charleston Battery and Seattle Sounders FC, playing 90 minutes and contributing two assists in Dynamo's 4-0 win over Charleston. Hayden was waived by Houston on November 25, 2009.
In January 2010, Hayden signed with his hometown's Louisville Lightning from the Professional Arena Soccer League. He also returned to the Lightning for the full 2010-11 season.
A two-time Parade Magazine All-American at Trinity High School in Louisville, Kentucky, Hayden matriculated at Indiana University in 2002. After redshirting his freshman season, Hayden began to see regular time with the Hoosiers in 2003 as they won back-to-back NCAA titles in 2003 and 2004, the latter in penalties versus the University of California, Santa Barbara. His biggest moment came in the 2004 NCAA College Cup semifinals, when he scored an overtime header in Indiana's win over third-ranked Maryland. Hayden scored a career-high seven goals his sophomore year. Hayden was a regular in the midfield as a junior in 2005 as well before completing his career with an all-Big Ten Conference season in 2006.
While at Indiana, Hayden spent the collegiate off-season with several USL Premier Development League teams. In 2002 and 2003, he played with the West Michigan Edge. In 2004, he spent the season with the Indiana Blast and in 2005 with the Chicago Fire Premier. Hayden signed with the Fort Wayne Fever for the 2006 season.
On December 1, 2007 Hayden married Hollie Minogue, who played soccer for the University of Louisville women's soccer team.