Giacchino was born in Riverside Township, New Jersey. His father's ancestors came from Sicily and his mother's ancestors emigrated from Abruzzo in the center of Italy; he holds dual American and Italian citizenship. Giacchino grew up in Edgewater Park Township, New Jersey. He graduated from Holy Cross High School in Delran Township, New Jersey in 1986.

Giacchino enrolled at SVA, majoring in film production and minoring in history. During his final year at SVA, his instructor in film publicity announced an unpaid internship was available at Universal Pictures. Giacchino, who was the only one interested, obtained the six-month position, which he filled at night while attending school during the day and working at Macy's to pay his rent. He graduated from SVA in 1990 with a Bachelor of Fine Arts, after which he took music classes at the Juilliard School.

Giacchino's composition work for Disney Interactive during the 16-bit era included the Sega Genesis game Gargoyles, the SNES game Maui Mallard in Cold Shadow and the various console versions of The Lion King. However his first major composition was for the DreamWorks video game adaptation of the 1997 movie, The Lost World: Jurassic Park. The video game was one of the first PlayStation- (also on Sega Saturn) console title to be recorded with an original live orchestral score. Giacchino has since continued his relationship with DreamWorks which also included composing the score for the Small Soldiers video game in 1998, providing full orchestral scores for many of their popular videogames. He also worked with Pandemic studios to create the theme for Mercenaries: Playground of Destruction. Giacchino's award-winning compositions covers the first four instalments of the Medal of Honor series, (Medal of Honor, Underground, Allied Assault and Frontline), Heroes: 2, and also the scores for several other World War II-related video games like Secret Weapons Over Normandy, Call of Duty and Call of Duty: Finest Hour. Additionally, Giacchino composed themes for The Incredibles: Rise of the Underminer, and co-wrote the theme of Black with Composer Chris Tilton. He also composed the score for Alias, which was based on the television series of the same name. In 2008 Giacchino wrote music for Turning Point: Fall of Liberty. In 2007, he returned to the Medal of Honor franchise as he composed the music for Medal of Honor: Airborne.

In 2001, J. J. Abrams, Producer of the television series Alias, discovered Giacchino through his video game work and asked him to provide the new show's Soundtrack. The Soundtrack featured a mix of full orchestral pieces frequently intermingled with upbeat electronic music, a departure from much of his previous work. Giacchino would go on to provide the score for J.J. Abrams's 2004 television series Lost, creating an acclaimed score which employed a unique process of using spare pieces of a plane fuselage for percussion parts. The score for Lost is also notable for a signature thematic motif: a brass fall-off at the end of certain themes. Just like his counterpart Stu Phillips, he worked with the television show creator Abrams on his shows with his music scores while Abrams supplied the show's main themes on certain series such as Alias.

In 2004, Giacchino received his first big feature film commission. Brad Bird, Director of Pixar's The Incredibles, asked Giacchino to provide the Soundtrack for the film after having heard his work on Alias. The upbeat jazz orchestral sound was a departure in style not only for Giacchino but for Pixar, which had previously relied on Randy and Thomas Newman for all of its films. Director Brad Bird had originally sought out John Barry – perhaps best known for his work on the early James Bond films—but Barry was reportedly unwilling to repeat the styles of his earlier works.

In addition to his long list of soundtracks, in 2005 Giacchino collaborated with Walt Disney Imagineering in creating two new soundtracks for the updated versions of Space Mountain at Disneyland, Space Mountain: Mission 2 at Disneyland Paris, and Space Mountain at Hong Kong Disneyland. Giacchino was also contracted by Sarah Vowell, who played character Violet in The Incredibles, to compose the score to the audio version of her book Assassination Vacation. Michael Giacchino's music can also be heard in "Star Tours: The Adventure Continues" during the "travel log videos" shown in the queue for both the Disneyland and Walt Disney World versions of the attraction.

In 2009, he was asked to conduct the Academy Awards orchestra for the 81st Academy Awards. For this project he rearranged many famous movie themes in different styles, including a 1930s Big Band treatment of Lawrence of Arabia and a bossa nova of Moon River. Giacchino also composed the fanfare for the 100th Anniversary logo for Paramount Pictures.

Giacchino is noted for using humorous titles filled with puns on his Soundtrack albums. Dawn of the Planet of the Apes and Jurassic World in particular had many ape and dinosaur-related double entendres such as "Gorilla Warfare" and "Raptor Your Heart Out". Many of those have references to previous works of his, both in style and naming. Giacchino used themes from the track "U-Boat" from the Medal of Honor Soundtrack in the tracks "Sawyer Jones and the Temple of Boom" and "Sub-Primed" from the 5th and 6th season Lost soundtracks as the submarine motif. In terms of naming, the score for The Incredibles contains a piece named "100 Mile Dash", and subsequently Ratatouille had "100 Rat Dash", Up had "Three Dog Dash", and Coco had "Shrine and Dash". Another series of examples: "World's Worst Beach Party" from the first Lost album, "World's Worst Last 4 Minutes To Live" from the Mission: Impossible III Soundtrack, "Galaxy's Worst Su Shi Bar" from Star Trek (2010 deluxe release), "World's Worst Landscaping" from the second Lost album, "World's Worst Car Wash" from the Soundtrack album Lost: The Final Season, and "World's Worst Field Trip" from the Soundtrack of Super 8. The Soundtrack for Mission: Impossible – Ghost Protocol also has a track titled "World's Worst Parking Valet", and the score for Zootopia contains a track titled "World's Worst Animal Shelter". Inversely, the score for Mercenaries: Playground of Destruction has a track entitled "World's Best Carpool Lane"; the Speed Racer score has tracks entitled "World's Best Autopia" and "World's Worst Road Rage."

In November 2015, it was announced that Giacchino would be returning to Pixar to score The Incredibles 2.

In 2016, Giacchino composed the score for the Marvel film Doctor Strange, as well as the score for the Disney film Zootopia. In September 2016, it was announced that Giacchino had been chosen to replace Composer Alex Andre Desplat as the Composer for the Star Wars anthology film, Rogue One, after Desplat was unavailable following reshoots. Giacchino then scored another Marvel Studios film, 2017's Spider-Man: Homecoming.