In Apr., 1920, Pu-Jiang-Tou Public School established San Kun Dian Branch by order. Mr. Chen Fu Yuan was designated Supervisor of the branch, who was one of the first two teachers and later served as the chief of the Yong Kang Township Farmer's Association.

On Apr. 1, 1921, it was renamed Yong Kang Public School San Kun Dian Branch.

In 1924, due to the school ground donation from Mr. Huang Fen, Mr. Chen Si Cyuan and Mr. Yang Nan Hai, the school was moved to the present location.

On Apr. 1, 1941, the school was independent of San Kun Dian Civil School.

In 1945, Taiwan was restored. It was renamed Yong Kang the Third Elementary School. Mr. Jheng Wan Ding was appointed as the first-term principal.

From Apr., 1946, to Aug., 1947, Mr. Lin Fun Lai was delegated to be the second-term principal.

On Feb. 1, 1947, it was renamed Yong Kang Township San Cun Elementary School.

From Sep., 1947, to Jan., 1962, the third-term principal, Mr. Chen Jiang Long served as the longest-term principal.

From Mar., 1962, to Jul., 1966, Mr. Wu You Bian served as the fourth-term principal.

From Nov., 1966, to Aug., 1975, Mr. Chen Pen was the fifth-term principal.

On Aug. 1,1968, compulsory education was lengthened to nine years. It was renamed San Cun Elementary School.

From Sep., 1975, to Jan., 1993, Mr. Sie Sian Pei was designated as the sixth-term principal.

In 1976, Mr. Huang Jin Teng and Mr. Huang Yan Ming donated 19 square meters of land to school, which was valued at 200 thousand dollars at that time.

From Aug., 1988 to Jan., 1993, Mr. Jhuo Jheng Fang was delegated as the seventh-term principal.

From Feb., 1993 to Jan., 2001, Mr. Fan En served as the eighth-term principal.

On May. 1, 1993, the school was renamed Yong Kang City San Cun Elementary School.

From Feb., 1991 to Jul., 1991, Supervisor of Tainan County Education Bureau, Lin Dong Jheng was assigned as the deputy principal.

From Jul., 2001 to Jul., 2008, Mr. Yen Yong Chin served as the nitnth-term principal.

From Aug., 2008 to Jul., 2016, Mr. Shen Kun Hung served as the tenth principal.

On Dec. 25, 2010, Tainan County and Tainan City were merged into the Tainan special municipality. The the school was renamed Tainan Municipal San Cun Elementary School.

From Aug., 2016 to Jul., 2018, Mr. Chen Rui Fang served as the eleventh principal.

From Aug., 2018 to Jul., 2024,Mr. Huang Chun Chieh has been serving as the twelfth principal.

Ms. HO LI-YU has been serving as the thirteenth principal since Aug., 2024.