After the Second World War, Tamsui Middle School and Tamsui Girls' School were returned to the church for management. According to regulations such as the <i>Private Secondary School Management Rules in Taiwan Province</i> stipulated by the Nationalist government, private schools were required to organize a board of directors for the administration of the school. Therefore, the Presbyterian Church appointed Lin Mao¬-sheng as the Chairman of the Board and Acting Principal. Under this new structure, the operation of Tamsui Middle School and Tamsui Girls' School gradually got on track. In early 1947, the 228 Incident occurred. Chairman Lin Mao-sheng and Principal Tân Lêng-thong, along with some other teachers and students, were involved, affecting the school’s administration and sending it into a period of turbulence.

During the 228 Incident, classes at Tamsui Middle school were suspended, and it wasn't until April 16th that the school reopened. The Taipei City mayor at the time, Yu Mi-¬chien, was assigned as the chairman and principal of the school. Tamsui Middle School and Tamsui Girls' School were merged to form the boys’ and girls’ divisions of Private Tamkang High School.

In March 1948, the administration of boys’ and girls’ divisions at Tamkang High School was once again separated. Subsequently, Tamkang High School went through another tumultuous period, marked by changes in ownership, mergers and divisions. Within six years, ten different principals were replaced or suppressed by the government. This instability was also reflected in the students' performance. For example, the formerly dominant Tamkang High School rugby team didn't perform as wonderfully as it did before.

Not until 1955 did the turbulent situation gradually stabilize. The two schools, for boys and girls, proceeded again with preparations to merge and were combined into Tamkang High School in 1956, which has developed steadily ever since.