Petrucci first played guitar at age 8 when he noticed his sister (who was taking organ lessons at the time) was allowed to stay up past her bed time to practice. He soon dropped it when his plan failed. At age 12, he began playing again when he was invited into the band of his friend Kevin Moore, who would later become the first keyboardist of Dream Theater. Petrucci began to practice in earnest whilst exercising physically. He was a largely self-taught guitarist who developed his skills through attempts to match the skill of his idols, who included Steve Morse, Steve Howe, Steve Vai, Stevie Ray Vaughan, Al Di Meola, Alex Lifeson and Allan Holdsworth. He has jokingly referred to his guitar idols as "the Steves and the Als".
Petrucci attended Berklee College of Music in Boston with childhood friend John Myung (bass), where they met future bandmate Mike Portnoy (drums). These three in addition to another childhood friend of Petrucci and Myung, Kevin Moore (Keyboards), formed the band Majesty, which would later become Dream Theater.
While Dream Theater is what Petrucci is most commonly associated with, he is also a part of the project band Liquid Tension Experiment and has appeared as a guest on several records by other artists such as the Age of Impact album by the Explorer's Club.
Petrucci has released a guitar instructional video, "Rock Discipline", which covers warm up exercises, exercises to avoid injury while playing, alternate picking, sweep picking, chords and other techniques for developing one's guitar playing. Petrucci also has a book named "Guitar World presents John Petrucci's Wild Stringdom", which was compiled from columns he wrote for Guitar World magazine, bearing that same title.
In 2001 he was invited by Joe Satriani and Steve Vai to tour with them on the popular G3 guitar tour, which exposed him to a massive number of new fans and inspired him to record a solo album. Suspended Animation was released on March 1, 2005, and made available for order from his web site. He also appeared on the 2005, 2006 and 2007 G3 tours.
Petrucci also wrote and recorded two instrumental soundtrack songs for a Sega Saturn game titled Digital Pinball: Necronomicon. Each track is roughly two minutes long and they are simply titled "Prologue" and "Epilogue". Petrucci is an avid Sega Saturn gamer, and has revealed in interviews that he never tours without one.
In 2007, John Petrucci went on G3 tour again, this time with Joe Satriani and Paul Gilbert.
Dream Theater bandmate Jordan Rudess revealed in an interview that Petrucci is a practicing Catholic. Petrucci is married to Rena Sands, a guitarist in the all-female heavy metal band Meanstreak, and they have 3 children, SamiJo, Reny (who are twins) and Kiara.