Gonzalo Julio González Fonseca was born on May 27, 1963, in Havana, into a family of musicians, and took the professional name Rubalcaba from his great-grandmother, as his father and grandfather had before him. His father, Guillermo Rubalcaba, was a pianist, composer and bandleader who played in Enrique Jorrín's orchestra and later led Charanga Rubalcaba, and his grandfather Jacobo wrote danzones. Gonzalo began as a drummer in his father's orchestra at about the age of six, started formal study two years later and chose the piano as his main instrument. He trained at Havana's Manuel Saumell and Amadeo Roldán conservatories and studied composition at the Instituto Superior de Arte, and by his mid-teens he was working as a drummer and pianist in hotels, concert halls and jazz clubs. Despite the U.S. embargo, jazz records and American radio reached the island, and he took in Art Tatum, Count Basie, Charlie Parker and Dizzy Gillespie that way.

In 1983 he toured France and Africa with the charanga and salsa orchestra Orquesta Aragón, and in 1985 he formed his own band, Grupo Proyecto, which mixed Afro-Cuban rhythm with jazz-rock. That year Gillespie heard him at the Jazz Plaza festival in Havana and is reported to have called him the best jazz pianist he had heard in more than a decade; a live album from the festival, Gillespie en vivo, with Gillespie and Rubalcaba, came out in Cuba on the Areito label. In 1986 the bassist Charlie Haden, in Havana for the festival, and the Blue Note Records president Bruce Lundvall heard him, and the German label Messidor issued three albums by his Cuban group, Mi Gran Pasión (recorded in 1987), Live in Havana and Giraldilla (1990). Haden brought him to the Montreal jazz festival in 1989 to play in a trio with the drummer Paul Motian, a set recorded on July 3, 1989, and released in 1997 as The Montréal Tapes, and in July 1990 Rubalcaba joined the same two at the Montreux festival, the performance that became Discovery: Live at Montreux.

For several years the U.S. government kept him out of the country, and Gillespie, Haden and Wynton Marsalis lobbied on his behalf. He first performed in the United States in 1993, after Gillespie's death that January: Gillespie's widow, Lorraine, invited him to serve as a pallbearer, which brought him a visa, and he followed with a trio concert with Haden and Jack DeJohnette at Lincoln Center's Alice Tully Hall on May 14, 1993, one piece of which appears on Imagine. In the early 1990s he had moved to the Dominican Republic, which let him accept paid work abroad while he kept his Cuban citizenship, and in 1996, with the Cuban government's permission, he moved his family to South Florida, where he has lived since. Blue Note issued most of his records of the decade and a half that followed: The Blessing (1991) with Haden and DeJohnette, the live Images (recorded at the Mt. Fuji Jazz Festival in August 1991 with the bassist John Patitucci and DeJohnette), Suite 4 y 20 (1992, recorded in Madrid, with Haden on five tracks), Rapsodia (1993), the Gillespie tribute Diz (1994), a trio album with the bassist Ron Carter and the drummer Julio Barreto, Imagine (1995), Antiguo (1998; recorded with his Cuban quartet and synthesizers), which was nominated for a Grammy for Best Latin Jazz Album, and Flying Colors (1998), recorded with Joe Lovano.

The partnership with Haden became a second career. Nocturne (Verve, 2001), a set of Cuban and Mexican boleros and ballads recorded in Miami in August 2000, with Rubalcaba as co-producer, won the Grammy for Best Latin Jazz Album at the 2002 ceremony, and Land of the Sun (2004), Mexican dance music from the 1940s that Rubalcaba arranged for an ensemble of ten including Lovano and Miguel Zenón, won the same award in 2005; Rubalcaba was credited on both awards as producer. The two also recorded Tokyo Adagio live at the Blue Note in Tokyo in 2005, released in 2015 after Haden's death in 2014, and Rubalcaba made his own tribute to Haden on Charlie (2015). His trio with the bassist Carlos Henríquez and the drummer Ignacio Berroa made Supernova (Blue Note, July 17, 2001), which won the Latin Grammy for Best Latin Jazz Album, and the solo album Solo (Blue Note, March 7, 2006) won the same Latin Grammy in 2006. In these years he also recorded with Pat Martino (Think Tank, 2003, a Blue Note quintet with Lovano, Christian McBride and Lewis Nash), played duets with Chick Corea (Rendezvous in New York, 2003), and joined Dave Holland, Chris Potter and Eric Harland on the live Monterey Quartet album from the 2007 Monterey Jazz Festival.

In 2010 he co-founded the record label 5Passion with the businessman Gary Galimidi, and it issued Fe (2010), XXI Century (2011), Suite Caminos (2015), which was nominated for a Grammy for Best Latin Jazz Album, and Charlie. He joined the faculty of the University of Miami's Frost School of Music in 2015, where the university's directory lists him as a lecturer in studio music and jazz, and in 2020 he started the Rubalcademy, an online masterclass program. Skyline (5Passion, September 17, 2021), a trio album with bassist Carter and drummer DeJohnette, won the Grammy for Best Jazz Instrumental Album at the 2022 ceremony. His later projects include Pédron Rubalcaba (2023) with the French saxophonist Pierrick Pédron, the solo-piano Borrowed Roses (2023), COLLAB (2024) with the Brazilian mandolinist Hamilton de Holanda, which was nominated for a Grammy for Best Latin Jazz Album, and First Meeting (2025), recorded live at Dizzy's Club in New York in August 2022 with Potter, Harland and the bassist Larry Grenadier. A Tribute to Benny Moré and Nat King Cole, made with Yainer Horta and Joey Calveiro, won the Grammy for Best Latin Jazz Album at the ceremony held in 2026, and on Filin (Blue Note, February 13, 2026) he played piano and wrote the arrangements for Melissa Aldana's album of Cuban ballads. In 1999 Piano & Keyboard magazine named him one of the great pianists of the twentieth century, and in 2008 the ASCAP Foundation gave him its Vanguard Award.

Rubalcaba plays with a conservatory pianist's command of the instrument and a percussionist's sense of the beat, and he has described the piano as part of the percussion family; his early training as a drummer shows in the way he displaces rhythmic and harmonic patterns against the guajeo, the repeating figure of Cuban dance music. A 1996 JazzTimes profile heard in him a blend of Oscar Peterson, Chucho Valdés, McCoy Tyner and Franz Liszt, and his own listening as a young man ran through Art Tatum, Charlie Parker and Dizzy Gillespie. He writes for formats from solo piano and trio to ten-piece ensembles and the eight-section Suite Caminos, and he moves between Cuban material (boleros, danzón, filin), Mexican and Brazilian songs, standards and his own compositions, often within one program. Critics have counted him among the leading figures of Afro-Cuban jazz and among the post-bop pianists of his generation.