Warren was born on leap day (February 29) in Huntsville, Alabama. He is the son of Mervyn A. Warren, a university administrator, professor, and author, and Barbara J. Warren, a university professor who specialized in early childhood education. His mother taught him reading and math when he was three years old, which enabled him to complete the first and second grades in one year. Upon beginning the third grade, his classmates, thinking he had "skipped" a grade, taunted and ostracized him for the next several years. During that time, he immersed himself in playing the piano, which he had begun under his mother's tutelage at the age of five. He took piano lessons briefly between the ages of 6 and 10, but lost interest, preferring improvising to memorization. Because his parents are Seventh-day Adventists, he was forbidden from listening to pop music or rhythm and blues. He was punished at the age of twelve when he got caught with a copy of the album Gratitude by Earth, Wind & Fire. Instead he listened to easy-listening, contemporary Christian, classical, choral music, the Mantovani Orchestra, Edwin Hawkins, and the Swingle Singers. He grew up near Oakwood University, where he saw ensembles perform. At fifteen, he enrolled in a summer program at Alabama A&M University for high school students who excelled at math and science. In 1981 he was valedictorian at Oakwood Adventist Academy, then a few months later entered Oakwood University. He graduated in 1985 with a degree in music. Two years later he received a master's degree in arranging from the University of Alabama, having studied with Steve Sample Sr.

At the age of five, Warren began playing the piano by ear, after being taught a few songs by his mother. Thereafter, for many years he immersed himself in the piano, learning to play various styles by ear and creating new arrangements of existing pieces. As early as the age of seven, he was accompanying vocalists at the piano for their performances at school or church. He soon became sought after as an accompanist in the community and throughout college and graduate school.

At the age of 10, Warren became the regular accompanist for a vocal group composed of five of his female classmates where they performed regularly at school and community events. Within weeks of becoming their accompanist, Warren began creating original arrangements for the group. When he was 12, he was asked by a classmate if he had ever considered composing an original song. Though Warren had not previously considered doing so, the suggestion prompted him to begin composing original songs and lyrics which he taught to the vocal group and which they performed publicly.

Warren had an innate inclination toward jazz and complex harmony, which was evident in both his original songs and arrangements of existing songs. This propensity was met with disdain by some of the more conservative members of the Oakwood community, resulting in an ongoing struggle between figures of authority and Warren. At the age of 13, Warren expanded the five-voice, female vocal group to a nine-voice, mixed vocal group. This group, The Symbolic Sounds, sang his arrangements and compositions exclusively, and remained popular in the school and community through 1981.

Warren's first professional recording session was for a new version of "The Lord's Prayer", set to an original melody, which Warren co-wrote with his friend Eric Todd. It was recorded by Blessed Peace, a popular gospel choir at Oakwood University, at the Sound Cell Recording Studio in Huntsville, Alabama. Warren created the vocal arrangement, played keyboards, and assisted Todd with the overall production. During that session, studio-owner Doug Jansen Smith, took note of Warren's abilities. Soon, Warren became a regular session-performer at Sound Cell, contributing to arrangements, playing keyboards, and singing on the radio and TV while performing pop, rock, country, and contemporary Christian recordings.