John taught for nine years at Geelong Grammar School, and became Head of English at the school's Timbertop campus. In 1982, he was arrested while on the blockade attempting to stop construction of the Franklin Dam. As all the prisons in the region were full due to the number of people arrested, Marsden was placed in the high-security Risdon Prison for a night. He later wrote that he used the experience to help him write scenes in Letters From The Inside and parts of the Tomorrow series.
His landmark Tomorrow series is recognised as the most popular book series for young adults ever written in Australia. The first book of this series, Tomorrow When The War Began, has been reprinted 26 times in Australia. The first sequel of a new series of books featuring Ellie Linton from the Tomorrow series (The Ellie Chronicles) was published in 2003, with the second novel and third novels released in November 2005 and November 2006 respectively.