This paper aims to explore the disparity between the institutionalization and implementation of medical knowledge in the Meiji government's response to the cholera epidemic in the late 1870s, specifically focusing on the operation of the isolation hospital (Hibyoin). It looks like that the cholera epidemic in the late 1870s prompted the establishment of a series of fundamental laws regarding medical and sanitary practices, ostensibly aiming to create a legal framework based on modern Western medicine. However, the reality was quite different. One of the key preventive measures during the cholera epidemic was quarantine. However, the practice of isolating cholera patients in hospitals was only implemented for certain segments of the population, due to limited medical knowledge and widespread negative perceptions of isolation hospitals as typical quarantine spaces. Instead, measures such as traffic restrictions, cleanliness, disinfection, and adhering to a specific regimen were implemented for epidemic control. Shortly after the introduction of hospitals as medical care facilities for doctors to treat patients in the late 1860s, isolation hospitals, known as “Hibyoin,” were established as symbolic spaces for mandatory isolation. Although there was initially a negative perception about Hibyoin, these isolation hospitals eventually emerged as the primary medical institutions for patients with infectious diseases. This situation has changed significantly since the introduction of the 1897 Infectious Disease Prevention Act, whereby “Hibyoin” came to be referred to as “infectious disease hospitals” and were designated as legal institutions. Permanent infectious disease hospitals were established throughout the country based on the law. The institutionalization of permanent infectious disease hospitals demonstrates the political and societal consensus on the importance of such facilities for disease control. It reflects their transformation from a symbolic presence to a practical necessity based on real needs.