Munakata Shiko was born on September 3, 1903, in Aomori Prefecture, the third son of a blacksmith in a family of twelve children. 

Self-taught in European-style oil painting, the young Munakata often traversed the countryside sketching and painting landscapes mimetic of his idol, Vincent van Gogh. At the age of eighteen, he and his friends established the Seikokai (Blue Light Society), featuring in annual exhibitions for townsfolk. 

Despite his local celebrity, the highly-ambitious Munakata wanted to pursue a career as a professional artist. In 1924 he moved to Tokyo and worked as an itinerant shoe salesman and street peddler while painting in his spare time. In 1926, he discovered Kawakami Sumio's Early Summer Wind at a local gallery and became inspired to produce mokuhanga prints. In 1928, one of Munakata's oil paintings was accepted by the Teiten gallery, and Shimozawa Kihachiro, a fellow contemporary, introduced him to sosaku hanga artist Hiratsuka Un'ichi through his contacts at a local art magazine. Hiratsuka accepted Munakata as a student, however, the two men were opposed in terms of style, methodology, and temperament and soon after that parted ways. Not to be deterred, Munakata began exhibiting prints at Kokugakai from 1930 and served as an active member from 1932 to 1953. He also joined the Nihon Hanga Kyokai organization from 1932 to 1938 and displayed paintings at the Hakujitsukai, Bunten, and Teiten galleries. 

His early career was further augmented by the Folk Art movement after receiving the support of artists Yanagi Soetsu (whom he met in 1936) Kawai Kanjiro, and Hamada Shoji. Munakata, in turn, contributed to the literary magazines Shiro to Kuro, Han Geijutsu, Kitsutsuki, Chokokuto, Hosun Hanga, and Han. In addition, He founded the hanga art society Nihon Hanga-in (Banga-in) in 1952. 

Throughout his career, Munakata Shiko went on to achieve a degree of fame and international recognition that many of his fellow hanga artists did not. He won first prize at the Lugano (1952), São Paulo (1955), and Venice (1956) international biennales. From 1959 to 1960, he visited the United States and held solo exhibitions in various cities, widening his sphere of influence, courting the media, and developing his clientele base. Upon his return, Munakata was granted the rank of hokkyo, an ecclesiastical title awarded to lay artists by the Horin-ji temple in Kyoto. The following year, he was bestowed with the rank of Hogen by Nisseki-ji in Toyama Prefecture. He was later awarded the Medal of Honor in 1963, the Asahi Shimbun Cultural Prize in 1965, and the Order of Cultural Merit in 1970.