He studied at the Kaisei School in Tokyo and went to Britain (1876).
He was appointed a teacher at the Kobe Normal School (1879).
Sekiya took up the study of the earthquakes in 1880. In 1886, he was appointed as the first professor of seismology at what was to be the University of Tokyo, the first such full-time university appointment in the world. When a seismological observatory was built in the university, he became its first director. In this position, he helped in the extension of the seismic survey in Japan and in the erection of seismographs throughout the country. In 1886, the number of observing stations was over 600. In 1896, at the time of his death it had risen to 968.
Outside the scientific community, Sekiya is best known for the model representing the motion of the ground during an earthquake, inspired by the Tokyo earthquake of 1887. His earthquake model consists of three twisted copper wires that are mounted side by side on a lacquered wooden stand. The wire diagram gives an illustration of the complicated movements of the ground during an earthquake, conveying the complexity of ground motion, both in terms of the vagaries of its geometric path and in its erratic accelerations. Sekiya’s original copper-wire model now resides in the Whipple Museum of the History of Science at Cambridge University.
After spending several months studying the new crater and the devastated areas subsequent to 1888 eruption of Mount Bandai, he published together with Y. Kikuchi a report in English ("The eruption of Bandai-san" Tokyo Imperial University College of Sciences Journal 3 (1890), which is considered a classic in volcanology.
He collaborated with Sir James Ewing and John Milne, British seismologists who were professors at the university, in establishing seismology in Japan.