- Megatokyo 1 covering Chapter 0, published in March 2004
- Megatokyo 2 covering Chapter 1 and Chapter 2, published on 14 January 2004
- Megatokyo 3 covering Chapter 3 and Chapter 4, published in February 2005
- Megatokyo 4 covering Chapter 5 and Chapter 6, published in June 2006
- Megatokyo 5 covering Chapter 7 and Chapter 8, published on 23 May 2007
- Megatokyo 6 covering Chapter 9 and Chapter 10, published on July 20, 2010
The current publisher for the Megatokyo comics is DC Comics. Megatokyo 4 and 5 were published under DC Comics' now defunct manga imprint CMX, successive volumes will be released under the DC Comics imprint.
A series of prequel books, titles MegaTokyo: Endgames, is available in print, as Kindle e-books and for Barnes & Noble's Nook. These books are:
- The Tower of Kartage
- Dire Water
- Fire Fox
- The Daynish Campaign
- The Great Underground Empire (in development)
Megatokyo Vol. 2: Do You Want to Save Before You Quit? covering Chapter 1 and Chapter 2 (equivalent to Megatokyo 2), was planned to be published in April 2003, but never went to press.