Giovanni Hidalgo was born in San Juan, Puerto Rico, where he received his primary education. His grandfather was a musician, and his father, José Manuel Hidalgo "Mañengue", was a renowned conga player. Hidalgo was raised in a household surrounded by drums, bongos, congas, and timbales. For his eighth birthday, he received a conga which was handmade by his father. As a young child he practiced and developed his skills on the conga and on other instruments in his house. Hidalgo would drum a tune with sticks and then play the same tune with his hands. Hidalgo auditioned and was hired by the Batacumbele Band in 1980. In 1981, he traveled with the band to Cuba, where he met a musician by the name Changuito, a.k.a. José Luis Quintana. They created a style of rhythm that ushered in a new era in Latin music.  In 1985, Hidalgo was performing with Eddie Palmieri at the Village Gate in New York City when Dizzy Gillespie walked in and listened to him play. Gillespie was so impressed with Hidalgo that he told him that someday in the future they must get together and play. In 1988 Hidalgo joined Gillespie's United Nation Orchestra.  In 1992, Hidalgo was hired as an adjunct professor at the Berklee College of Music in Boston. He taught many types of rhythm: Puerto Rican, Cuban, Dominican, reggae, African, and jazz. He held this academic position until 1996.  During his career, he has worked with Bola Abimbola, Sikiru Adepoju, Art Blakey, Muruga Booker, Jack Bruce, Don Byron, Candido Camero, D'Angelo, Paulinho da Costa, Steve Gadd, Sammy Hagar, Kip Hanrahan, Zakir Hussain, Cassius Khan, Airto Moreira, Charlie Palmieri, Tito Puente, Hilton Ruiz, Paul Simon, and Carlos "Patato" Valdes.

On October 31, 2010, he performed with the rock band Phish during their Halloween concert. The band performed Waiting for Columbus by Little Feat with Hildalgo on percussion (with the exception of "Don't Bogart That Joint", which was performed a cappella) and a brass section of Aaron Johnson, Stuart Bogie, Ian Hendrickson, Michael Leonhart, and Eric Biondo. In 1991 Hidalgo received a Grammy Award for his contribution to the album Planet Drum (Rykodisc, 1991), performed by an ensemble of the same name led by Mickey Hart of The Grateful Dead. He played on another one of Hart's Grammy-winning albums, Global Drum Project and on the album Danzón (Dance On) (GRP, 1993) by Arturo Sandoval which won the 1995 Grammy Award for Best Latin Jazz Performance. Hands of Rhythm (RMM, 1997), Hidalgo's album with Michel Camilo, received a Grammy nomination, as did The Body Acoustic (Chesky, 2004), al album recorded by Hidalgo, David Chesky, Randy Brecker, Bob Mintzer, and Andy Gonzalez.  In May 2010, Hidalgo was awarded an Honorary Doctorate of Music from Berklee College of Music during the sixteenth consecutive year that faculty members from the school visited Puerto Rico for one of its global outreach programs.