MPN 3 was existed and operates since 1962 took place at SD Rapak (Now stand North Balikpapan sub district). The first had mastered on that time was Mr. M.L Maliangkay. Further more on 1966 SMPN 3 Moved to Kebun Sayur, occupies second hand China School building. With the same time SMP 4 and ST (technical school) was occupying the same building.

       Mr. M.L Malangkay (SMPN 3 Head master) was takes hold till 1972. After that on 1972 – 1988 SMPN 3 was leaded by Mr. Djumberi. On the 1978’s SMPN 3 was moved to Gn. Samarinda because of Fire Disaster happen on Kebun Sayur including SMPN 3 Building. On that time SMPN 3 was in phase of school development building.

 On the 1988 – 1996 SMPN 3 was lead by Mr. Ganda Sudarman. After that on 1996 was replaced by Mr. M. Amir was leading until 2003.

     SMPN 3 Balikpapan stands on ground for about 17847m²_, which provide with various facilities and basic facilities for supporting teaching and learning education system.