Born in 1435 as the fourth son of the 6th Muromachi shogun Ashikaga Yoshinori. He was ordained as a monk in childhood and became head priest of Tenryuji's Koinin sub-temple, but when the Kyotoku Disturbance erupted in 1454 — the Kamakura Kubo Ashikaga Shigeuji's assassination of Kanto Kanrei Uesugi Noritada plunging the Kanto region into chaos — the shogunate had Masatomo return to secular life in 1457 as a rival Kamakura Kubo to counter Shigeuji, sending him east in 1458. Unable to enter Kamakura against Shigeuji's resistance, he remained in Izu Province. In 1460, after his encampment at Kokusei-ji was burned by Shigeuji's forces, he established a residence at Horigoe in Tagata District, Izu (present-day Izunokuni, Shizuoka), thereafter known as the 'Horigoe Kubo.' His effective control never extended beyond Izu Province and its immediate surroundings, and he was never able to restore the true authority of a Kamakura Kubo. In 1482, the shogunate and the Koga Kubo (Shigeuji) reconciled, and Izu Province alone was confirmed as Masatomo's domain. In his later years he schemed to have his second son Yoshizumi, born to his consort Enman'in, become shogun, but he died of illness at the Horigoe residence on April 3, 1491, aged 57. Soon after his death, his eldest son Ashikaga Chachamaru staged a coup, murdering his half-brother Junjoji and Enman'in to seize headship, but in 1493 Ise Sozui (Hojo Soun) conquered the Horigoe residence, ending the Horigoe Kubo line after only one generation — the 'Izu invasion' that marked the beginning of the Later Hojo clan's expansion into the Kanto. Masatomo's line continued through his second son Yoshizumi, who became the 10th Muromachi shogun, and his descendants held the shogunate down to the 15th and final shogun, Ashikaga Yoshiaki.

Ordained as a monk in childhood, he was later returned to lay life and burdened with the heavy responsibility of Kamakura Kubo. Unable to win the support of the Kanto region's local warrior bands or even to enter Kamakura itself, he appears to have lacked strong political or military skill. In his later years he grew fixated on securing the shogunate for his son, leaving behind the seeds of a family succession dispute.

Though Masatomo's effective rule as Horigoe Kubo was quite limited, excavations at the site of his Horigoe residence in Izu (Den-Horigoe Gosho Ato) have revealed a garden pond complete with a winding stream and cascade, evidence of the refined, capital-style life befitting a Kubo, and the site is now a National Historic Site. After Masatomo's death, Ise Sozui (Hojo Soun) destroyed his son Chachamaru and seized Izu, using the region as a springboard for the Later Hojo clan's expansion into the Kanto and laying the foundation of that great Sengoku daimyo house. Masatomo's own bloodline continued through his second son Yoshizumi, the 10th shogun, down through the Muromachi shogunal line to the 15th and final shogun, Yoshiaki, at the close of the era.