Hammett was born on November 18, 1962 in San Francisco, and raised in the town of El Sobrante, California. He is the son of Teofila "Chefela" (née Oyao) and Dennis L. Hammett (a Merchant Marine). His mother is of Filipino descent and his father was of English, German, Scottish and Irish ancestry. He attended De Anza High School in Richmond, California. While attending De Anza High School, he met Les Claypool of Primus, and they remain close friends.
Hammett has a well-known passion for horror movies that stretches back to the late Sixties. After spraining his arm in a fight with his sister at the age of five, Hammett's parents placed him in front of the television. It was during this time that he first watched The Day of the Triffids. After that, Hammett found himself drawn to his brother's Frankenstein figures, and soon began spending his milk money on horror magazines. For the better part of the next decade, Hammett dove deep into the horror scene.
Hammett began showing an interest in music after listening to his brother Rick's extensive record collection (which included Jimi Hendrix, Led Zeppelin and UFO). He began selling his horror magazines to buy music records, which led him to properly picking up the guitar at the age of fifteen. Hammett's first guitar was (in his own words) a "wholly unglamorous" Montgomery Ward catalog special, which was accompanied by a shoebox (with a 4-inch speaker) for an amp. After purchasing a 1978 Fender Stratocaster copy, Hammett attempted to customize his sound with various guitar parts, before eventually buying a 1974 Gibson Flying V. Hammett also took a job at Burger King as a youth, which he quit as soon as he had saved enough money to purchase a Marshall amplifier.