Shinohara studied at the Tokyo University of the Arts from 1952 to 1954, studying composition with Tomojiro Ikenouchi, piano with Kazuko Yasukawa, and conducting with Akeo Watanabe and Kurt Woess. From 1954 to 1960, he studied in Paris with Tony Aubin, Olivier Messiaen, Simone Plé-Caussade, Pierre Revel and Louis Fourrestier. From 1962 to 1964 he studied in Munich at the Hochschule für Musik and at the Siemens electronic studio; following this he studied with Bernd Alois Zimmermann and Gottfried Michael Koenig at the Rheinische Musikhochschule in Cologne and then with Karlheinz Stockhausen from 1964–65. He held a scholarship from the German Academic Exchange Service in 1966 and 1967 and won a scholarship from the Italian government in 1969. In 1971, he was awarded the Rockefeller Prize from the Columbia Princeton Electronic Music Center and in 1978 won a scholarship from the Dutch government.
He worked with electronic music at the Institute of Sonology in Utrecht, at the electronic studio at the Technischen Universität in Berlin, at the Columbia Princeton Electronic Music Center in New York (1971–72) and at Studio NHK (Nippon Hōsō Kyōkai) in Tokyo. In 1978 Shinohara was a visiting professor of composition at McGill University in Montreal, Quebec, Canada (Rea 2008).
Since the 1970s, he has been best known for combining Western and traditional Japanese musics, as well as versatile experimentation with Western acoustic and electronic music (Herd 2001).
- 1975 Egalisation for 24 instruments (piccolo, flute, alto flute, oboe, English horn clarinet, bass clarinet, trumpet, trombone, tuba, piano, celesta, cembalo, harp, guitar, vibraphone, marimba, percussion, violin, viola, cello, and double bass)
- 1970 Visions for 3 flutes, 4 oboes, 4 clarinets, 4 bassoons, 4 horns, 4 trumpets, 4 trombones, 6 percussion, harp, celesta, 24 violins, 8 violas, 8 cellos, 4 double basses
- 1975 Visions II
- 1977 Liberation for 20 string instruments
- 1992 Yumeji (Ways of Dreams) for an orchestra of Japanese and Western instruments and mixed choir
- Solitude pour orchestra
- 1982/1985 Play for Nine Wind Instruments (flute, alto flute, oboe, clarinet, bass clarinet, bassoon, horn, trumpet, and trombone)
- 1958 Sonata for violin and piano
- Allegro moderato
- Allegro brutale
- 1960 Obsession for oboe and piano
- 1968 Fragmente for tenor recorder
- 1970 Reflexion for solo oboe
- 1983/1993 Turns for violin and koto
- 1984 Tabiyuki (On travel) for mezzo-soprano and small ensemble (flute, oboe, clarinet, bassoon, horn, trumpet, trombone, percussion, violin, viola, cello and double bass)
- 1986/1990 Evolution for solo cello
- 1990 Cooperation for 8 traditional Japanese and 8 Western instruments (English horn, clarinet, trumpet, trombone, percussion, piano, violin, and cello)
- 1993 Situations for alto saxophone and digital keyboard
- 2005 Turns for violin and koto
- Consonance for flute, horn, vibraphone, marimba, harp and cello
- Relations for flute and piano
- 1962 Alternance
- Elevation for organ
- 1963/1969 Tendence pour piano
- 1996 Undulation A for piano
- The Bear who saw the Sea for two pianos
Music for traditional Japanese instruments
- 1972 Tatuyai (Fluctuation) for koto, percussion, and singer
- 1972 Tuyatai (Fluctuation) for sangen
- 1973 Kyudo A (In quest of enlightenment) for shakuhachi
- 1973 Kyudo B for shakuhachi and harp
- 1981 Jushichigen-no-Umare (Birth of the bass koto) for 17-Gen
- 1981 Nagare for Shamisen for shamisen, sangen, kin and gongs
- Herd, Judith. 2001. "Shinohara, Makoto." The New Grove Dictionary of Music and Musicians, second edition, edited by Stanley Sadie and John Tyrrell. London: Macmillan Publishers.
- Landy, Leigh. 1987. "An Analysis of Tayutai for Koto (1972) Composed by Makoto Shinohara". Interface: Journal of New Music Research 16:75-96
- Rea, John. 2008. "Better Than a Thousand Days of Diligent Study Is One Day with a Great Teacher: Visiting Foreign Artist Residencies at McGill's Faculty of Music, 1975–1981". In Compositional Crossroads: Music, McGill, Montreal, edited by Eleanor V. Stubley. Montréal: McGill-Queen's University Press. ISBN 0-7735-3278-1
- Shinohara, Makoto. 2003. "Zusammenspiel westlicher und japanischer Instrumente". In Komposition und Musikwissenschaft im Dialog. III (1999–2001), edited by Imke Misch and Christoph von Blumröder. Signale aus Köln 6. Münster: Lit-Verlag.