Joan Sebastian was born in the rural town of Juliantla in Guerrero, and began composing at the age of seven. His mother had enrolled him to a school near Guanajuato when he was eight years old, and later returned to his hometown three years later.  At age fourteen, his mother sent him away to a monastery in Morelos where he was under the care of Father David Salgado. Due to the clergyman’s influence on Sebastian, he considered becoming a priest. He enrolled in the Seminario Conciliar de San José in Cuernavaca, Morelos, but realized that he wanted to pursue a music career, and decided to leave the seminary to dedicate himself to music.  Before embarking on a singing career, Sebastian was an administrative assistant at a vacation resort in Oaxtepec, Morelos, where he would sing through the intercom. In 1968, Sebastian met Mexican actress Angelica Maria. They stayed together and she asked him to sing some songs for her. She suggested to Sebastian that he record the songs and give them to music producer Eduardo Magallanes, though Sebastian never managed to contact him. He later moved to Mexico City and began asking Discos Capitals Records to listen to his music and produce it. In 1974, he recorded his first album, Pedro Parrandas, and received positive feedback from the public.

In 1977, Sebastian decided to stop using his legal name, Jose Manuel Figueroa and took on his artistic name, Joan Sebastian, partly in tribute to San Sebastian, where he previously worked. That same year, he signed a record deal with the label Musart. In 2000, he released Secreto de Amor which was certified 4× platinum in the Latin field in the United States by the Recording Industry Association of America (RIAA). The album and title track won the Lo Nuestro Awards for Regional Mexican Album of the Year and Regional Mexican Song of the Year; he also received the Excellence Award for his musical contributions.  In 2006, Sebastian was inducted into the Billboard Latin Music Hall of Fame for his prolific songwriting and musical arrangements. Sebastian was awarded Songwriter of the Year three times by ASCAP and received the Golden Note Award in 2007 in recognition of his songwriting career.

Sebastian was the father of eight children by five different partners. Their names are José Manuel Figueroa (who is also a singer and composer), Juan Sebastián, Trigo de Jesús, Sarelia, Julián (son of Maribel Guardia), Marcelia, Joana Marcelia and Julird. His oldest son, Trigo was shot in the back of the head after one of Joan Sebastian’s concerts in Texas on 27 August 2006. Trigo had been trying to control the crowd after the show. He was transported to McAllen Medical Center where he was pronounced dead.  On 12 June 2010, Juan Sebastián was shot dead in Cuernavaca, Morelos, after arriving at a night club with some friends and being refused entrance. Joan Sebastian said his son’s death had nothing to do with the Mexican drug cartels.  Sebastian was first diagnosed with bone cancer in 1999. He underwent cancer treatment and survived; however, he announced that the cancer had returned in 2007. Undergoing cancer treatment once again, he later announced he was in remission. On 26 July 2012, during one of his concerts, he announced that the cancer had returned for the third time. In 2014, he revealed that he was battling cancer for the fourth time during his performances in Zacatecas.  Weeks prior to his death, he confirmed to the media that he had been hospitalized and undergoing cancer treatment under medical supervision. On 13 July 2015, Joan Sebastian died at 7:15pm (UTC-06:00) at his ranch in Cruz de la Sierra, Teacalco Guerrero, Mexico, due to bone cancer. He was 64 years old.