Malone began his teaching career in 1993 as a paraprofessional and substitute teacher in the Boston Public Schools. He then worked as a high school social studies teacher in Boston from 1995 to 1999 and middle school assistant principal in Duxbury, Massachusetts from 1999 to 2000. From 2000 to 2003 headmaster of Monument High School, a new high school created from the breaking up of the large South Boston High School. From 2004 to 2005, Malone served as special assistant to the superintendent and instructional leader in the San Diego Unified School District. In this role he led the largest high school conversion initiative in the country. In 2005, Malone returned to Massachusetts as Swampscott, Massachusetts' superintendent of schools. In 2008, he informed the Swampscott school committee that he did not intend to renew his contract when it expired in 2010, citing a desire to return to an urban school district. Malone was a finalist for the superintendent's positions in Worcester and Springfield, Massachusetts.
Brockton
On June 23, 2009 the Brockton school committee voted 4 to 3 to hire Malone as superintendent of Brockton Public Schools. During Malone's tenure as superintendent, he had to cut $12 million from the department budget and lay off almost 150 employees. Student performance at the high school and middle school level improved, but elementary school MCAS test lagged. At Malone's 2012 annual review, the school committee gave him a composite score of 2.77 out of 5. On November 7, 2012, Malone and the Brockton School Committee agreed to end his contract early. The early termination did not include a buyout or severance package. Both Malone and the school committee stated that the city's residency requirement contributed to his departure.
On December 13, 2012, Governor Deval Patrick announced that Malone would replace Paul Reville as state education secretary. He was sworn into office on January 14, 2013.
Post-secretary career
In December 2014, Malone announced that he was planning to do an unpaid internship as a butcher following the end of Deval Patrick's term as governor. He also did some volunteer work and interviewed for college presidency positions. On October 8, 2015, the Saugus, Massachusetts school committee voted 3 to 2 to appoint Malone as interim superintendent. On February 5, 2016, attorneys for Malone and the school committee announced that Malone was resigning effective February 26 due to he and the committee having differing views on the role of a superintendent and the needs of the Saugus school system. On June 22, 2016, the Fall River school committee appointed Malone as the district's superintendent.
