Shrine was established at its current location according to the law that dictates "with the palace in the center, Jongmyo Shrine shall be established to its left, and Sajikdan Altar to its right" in 1395 (the 4th year of King Taejo), after the foundation of the Joseon dynasty (1392). At the time of the establishment, there was only the throne hall, so it was called Daemyo, Taemyo, or Jongmyo Shrine.
As a princely state, the Joseon dynasty honored the king`s ancestors according to the omyoje (a system of honoring the four generations of the present king` ancestors and the founding king). Then, when the omyoje system came to a halt during King Sejong’s period (1418–1450), a separate shrine was built next to the throne hall and named it Yeongnyeongjeon Hall.
Tablets succeeding four generations were moved to Yeongnyeongjeon Hall. Later, they were honored according to the law of sesil (hosting ancestral tablets for generations in the throne hall) and jocheon (moving tablets to Yeongnyeongjeon Hall) in the King Yeonsan period (1494–1506).
According to this legal system, the royal tablets that finished their three-year mourning period (27 months) were enshrined in the throne hall at the bumyorye ceremony (the honoring of their tablets). When the omyoje lapses, they are designated as either sesil or jocheon to be hosted in the throne hall or Yeongnyeongjeon Hall. This explains why the Jongmyo Shrine underwent several expansions, resulting in the present-day structure of 19 kan (the distance between two columns) for the throne hall and 16 kan for the Yeongnyeongjeon Hall.

Other facilities of the shrine include Mangmyoru Pavilion (where the officers of Jongmyo Shrine worked), Hyangdaecheong Hall (where incense and written ritual prayers were kept), Jaegung Hall (where kings and crown princes prepared for rituals), and Jeonsacheong Hall (where ritual foods were prepared).