Sylvia Cuenca was born and raised in San Jose, California, into a musical but non-professional household. Her father, a guitarist who sang Spanish boleros alongside jazz standards, kept a record collection heavy on jazz and Latin LPs; her mother knew the lyrics to dozens of standards, and her brother played guitar, bass, and mandolin. One record in her father's collection, Clifford Brown and Max Roach's Clifford Brown and Max Roach at Basin Street, became the spark: hearing Roach's clearly articulated solo, outlining form and melody on the drums, sent her looking for more. She has also traced part of her heritage to Tarahumara ancestry on her maternal grandmother's side, from the Chihuahua region of Mexico.

Cuenca took a snare drum class at Markham Junior High School in San Jose and followed it with private lessons, teaching herself the sound of a full drum set by ear from records. She spent her teenage evenings at the Garden City club, where pianist and jazz director Smith Dobson brought in touring names and let her sit behind the house drummer to watch. At 16 or 17 she joined the North Area Youth Jazz Ensemble as its second drummer. Her first professional engagement came alongside guitarist Eddie Duran and a young bassist named Larry Grenadier, booked into Pearl's in San Francisco's Chinatown. Not long afterward she won a scholarship to the first Stanford Jazz Workshop camp, where the faculty included Stan Getz, George Mraz, and drummer Victor Lewis; she attended for two years and then joined the staff herself, a position she has held since 1985, working alongside fellow drummers Billy Higgins and Albert "Tootie" Heath in the same period.

Victor Lewis, who had already relocated to New York, urged Cuenca to make the move herself, and on August 22, 1985, she flew from San Jose to JFK with her drums, cymbals, and a suitcase. She continued her education informally, studying on and off with Lewis, with Adam Nussbaum, with Keith Copeland (a year funded by a National Endowment for the Arts grant), and with the Brazilian drummer Portinho, whose lessons pulled her toward the bossa nova and samba-jazz repertoire she still plays. The NEA funded her studies again in 1988 and 1991, and in 1992 she reached the semifinal round of the Thelonious Monk International Jazz Drum Competition.

Her longest professional relationships both began within a few years of the move. She had first met tenor saxophonist Joe Henderson as a guest artist at San Jose City College; a year after arriving in New York she ran into him again at the Village Vanguard, said hello, and left her number. Three months later Henderson called to ask if she could tour Europe with him, a booking that reportedly grew out of his manager's suggestion of an all-woman band; Cuenca stayed in his working groups afterward regardless of that framing. Over roughly four years beginning in 1987, Henderson's quartet toured Norway, Denmark, Sweden, Austria, Belgium, England, Switzerland, France, Italy, and Germany, in addition to American dates, and Cuenca also worked in his trio, with Charlie Haden in 1989 and with George Mraz in 1994. That partnership is documented on the 1990 live album Punjab (ARCO Records), cut in a quartet with Henderson, pianist Renee Rosnes (misprinted "Irene Rosnes" on the original sleeve), and bassist Marlene Rosenberg. Alongside Henderson, Cuenca built a seventeen-year association with trumpeter Clark Terry, playing quintet and big-band dates with him at the Village Vanguard and the Blue Note on an annual basis, and on Royal Caribbean and S.S. Norway jazz cruises. That relationship produced several recordings, including The Hymn (2001, Candid), Top and Bottom (1997, Chiaroscuro, from the 1995 Floating Jazz Festival), Live on QE2 (2001, Chiaroscuro), Herr Ober: Live at Birdland Neuburg (2001, Nagel Heyer), and Louie & Clark Expedition 2 (2008, Percussion Power), a big-band co-billing with drummer/bandleader Louie Bellson.

Cuenca released her debut as a leader, The Crossing, in 1998 on her own label, Etoile Records, with a band built around trumpeter Eddie Henderson (a friend since she was 17, when he hired her for weekly gigs at Mikell's and Visiones and later toured her to Portugal), saxophonists Vincent Herring and Seamus Blake, pianist Dave Kikoski, bassist Essiet Essiet, and percussionist Gilad. She followed it in 2002 with Exit 13, a soul-jazz organ trio session on the same label with organist Kyle Koehler and guitarist Dave Stryker. Her broader sideman work runs through the Vienna Art Orchestra's Fe & Males (1992, Amadeo, alongside trumpeter Ingrid Jensen), the Ron McClure Quintet's Inner Account (1993, SteepleChase), Ted Curson's Traveling On (1997, Evidence), Frank Foster's Loud Minority Big Band, and organist Jared Gold's JG3+3 (2014, Posi-Tone). She married bassist Essiet Okon Essiet, who plays throughout much of her working discography and recording history, and the two continue to perform together on both coasts, including a long-running Sunday afternoon session at saxophonist Andrew Speight's Burlingame studio during the COVID-19 pandemic and reunion gigs with pianist George Cables and Eddie Henderson. In 2022 she recorded Wondering for Dot Time Records as the drummer in a co-billed trio with bassist Harvie S and guitarist Roni Ben-Hur. She continues to teach privately, at the Stanford Jazz Workshop, and at the San Francisco Conservatory of Music, and remains active on the bandstand on both coasts.

Cuenca describes her early education as listening her way through what she calls "the Magnificent Seven": Kenny Clarke, Art Blakey, Philly Joe Jones, Max Roach, Roy Haynes, Elvin Jones, and Tony Williams, absorbing each drummer's vocabulary one phrase at a time before Victor Lewis became her direct mentor and the strongest influence on her feel. The resulting style is a hard-swinging, post-bop/hard-bop attack built for the small-group and big-band mainstream: comfortable pushing a working quartet the way she did for Joe Henderson and Clark Terry, and, through her studies with the Brazilian drummer Portinho, equally at home in the bossa nova and samba-inflected material that surfaces throughout her discography, from Irio De Paula's West Orange to the bossa-nova and post-bop mix on Wondering.