Elena Pinderhughes was born in 1995 in Berkeley, California. Raised by professor and activist parents, she grew up in Berkeley with her older brother Samora, a pianist. She is biracial.

Inspired by her brother to pursue music, she was first drawn to the flute after attending a Venezuelan concert at age four, and she began singing and playing flute at age seven. From ages 8 to 18, she attended the Young Musicians Choral Orchestra academy in the East Bay, where she studied flute and voice with a focus in jazz and classical music. After being named a Presidential Scholar, she moved to New York to attend the Manhattan School of Music.

When Elena and Samora Pinderhughes were 9 and 13 years old respectively, they professionally recorded their first album together, entitled Catch 22. At age 10, Elena Pinderhughes was featured in the HBO special The Music in Me, in which she played Latin jazz flute alongside other young musicians.

Upon moving to New York for college, Pinderhughes was propelled into the city's jazz scene, where she met and began collaborating with musicians such as Ambrose Akinmusire, Chief Xian aTunde Adjuah, and Terri Lyne Carrington. In 2015, Chief Xian aTunde Adjuah (then performing as Christian Scott) released an album featuring Pinderhughes titled Stretch Music, which he subtitled (Introducing Elena Pinderhughes). In 2016, Pinderhughes was named the number one "Rising Star" flutist in DownBeat magazine.

In October 2016, Pinderhughes performed in Common's NPR Tiny Desk Concert at the White House, alongside Robert Glasper, Bilal, Karriem Riggins, Derrick Hodge, and Keyon Harrold. She has also appeared in Tiny Desk Concerts by Chief Xian aTunde Adjuah in 2015, Zaytoven in 2019, and her brother Samora Pinderhughes in a virtual concert in 2022.

In September 2023, Pinderhughes performed a five-part suite titled "A Diaspora Journey" alongside Beninese guitarist Lionel Loueke at the Monterey Jazz Festival. Pinderhughes and Loueke also both performed with Herbie Hancock for his headlining set at the festival.