The Japanese Starfighter was given the designation F-104J, the J standing for Japan.  It was similar in overall structure to the F-104G, but was equipped as an all-weather interceptor rather than as an air-to-ground strike aircraft.  One of the reasons for the choice of this option was that treaty restrictions at the time prevented Japan from acquiring any aircraft which had even a hint of an offensive role. 

The F-104J was powered by a Japanese-built J79-IHI-11A engine built under license by Ishikawajima-Harima.  It had an Automatics NASARR F-15J-31 fire control system optimised for the air-to-air mode, and was armed with a 20-mm M61A1 cannon and four AIM-9 Sidewinder air-to-air missiles, two mounted under the wing and two carried on a rack on the fuselage centreline. 

The first Lockheed-built F-104J (Model 683-07-14) flew on June 30, 1961.  Three F-104Js were built by Lockheed.  Deliveries of Mitsubishi-assembled F-104Js extended from March of 1962 through March of 1965, a total of 29 machines being delivered.  The delivery of Mitsubishi-manufactured F-104Js extended from March of 1965 through 1967.  A total of 178 F-104Js were constructed Mitsubishi. 

The F-104DJ (Model 583B-10-17) was the two-seat trainer version of the F-104J for Japan.  They had electronics and other items that were compatible with those of the single-seat version.  Twenty examples were built by Lockheed and reassembled in Japan between July of 1962 and January 1964.  No F-104DJ two-seaters were constructed by Mitsubishi 

The F-104J entered with the Koku Jietai (Japanese Air Self Defence Force, or JASDF) in October of 1966.  The first JASDF units to convert to the F-104J were the 201st and 202nd Fighter Interceptor Squadrons (Hiko-tais) based at Chitose and Nyutabaru.  The two hundred and ten F-104Js and the twenty F-104DJ operational trainers were used exclusively in the interceptor role by seven Hiko-tais (the 201st to 207th) of the Koku Jieitai. 

Beginning in December of 1981, the Japanese Starfighters were replaced by Mitsubishi-built F-15J/F-15DJ Eagles.  The last JASDF F-104J was retired by the 207th Hiko-tai in March of 1986.

After the retirement from the front line operation, some F-104s were used by ADTW(Air Development and Testing Wing) for miscellaneous duties such as chaser plane.

The last duties for JASDF F-104J were to be unmanned target drones. Two F-104Js were modified to UF-104J experimental drones and tested by ADTW. After that, 14 Starfighters converted to UF-104JA target drone and all of them were shot down at firing range located near Iwo-Jima.