After taking over Taiwan in 1895, the Japanese regime introduced a new education system. As a result, the Tamsui Girls' School was restructured in 1907, attracting many female students to enroll and ultimately playing a significant role in the history of female education in Taiwan. An example was Taiwan's first female physician, Dr. Tshuà A-sìn, a distinguished graduate Tamsui Girls' School.

Due to issues such as a lack of funding, Tamsui Middle School was not established until March 9, 1914, which coincided with the anniversary of Dr. Mackay's arrival. Both Tamsui Middle School and Tamsui Girls’ High School were founded with a religious spirit. However, the Japanese government prohibited schools from offering religious education. Additionally, it mandated that teachers and students participate in worship at Shinto shrines. Consequently, these two schools did not receive recognition from the Japanese government, and their students often had to leave school or went to Japan to pursue further studies after completing their senior years. These systemic constraints resulted in a growing number of students dropping out of Tamsui Middle School.

In 1934, as international tensions intensified, the Government General of Taiwan gradually strengthened its control over the country and adopted a more rigid educational policy. On August 15, 1936, the Japanese government took over the administration of Tamsui Middle School until the end of the Second World War. Despite being governed by the Japanese during its later years, the school administration put earnest efforts into education and with recognition from the Japanese government, Tamsui Middle School was eventually integrated into the formal education system. This allowed students to continue their further education, fostering a vibrant school atmosphere. Student enrollment increased, and the graduation rate was significantly improved.