This paper aims to study the quarantine system established by His Corean Majesty's Customs Service (HCMCS) between 1886 to 1893, and how they responded to the influx of infectious diseases such as cholera, led by the Customs Medical Officer of Joseon. The quarantine procedure was not able to operate in the first 11 years of opening the port due to limitations within HCMCS in the P. G. von Möllendorff period. However, as the Shanghai Customs officer, H. F. Merrill concurrently served as the Chief Commissioner, Seoul, HCMCS was directly connected to Shanghai Customs which was a direct model of Chinese Maritime Customs Service. This connection caused HCMCS to build a foundation that enabled the Shanghai quarantine measures to be referred to in 1886. In alignment with this, Acting Commissioner, Jenchuan, J. F. Schoenicke developed the quarantine system of Jenchuan Customs in 1886, using the quarantine system of Shanghai Customs as reference. Jenchuan Customs introduced new concepts, such as Observation Island, Yellow Flag, Free Pratique, and also enforced quarantine inspections on vessels coming from cholera-infected areas. Based on the quarantine system of the Shanghai Customs and Jenchuan Customs, Chief Commissioner, H. F. Merrill established conditions in 1887 for enforcing quarantine inspections on vessels arriving at the ports of Joseon. HCMCS conducted quarantine inspections on vessels coming from areas of infectious diseases, such as cholera, plague, yellow fever and smallpox, adopting concepts such as Customs Quarantine Officers, Quarantine boats, and Quarantine Hospitals. Quarantine hospitals affiliated with customs were founded at each trading port in order to treat patients with infectious diseases. Although His Corean Majesty's Hospital has been known as an 'only Western-style hospital' operated by the Joseon government, it should be noted that also these hospitals contributed medical activities. Meanwhile, document administration was accompanied to handle quarantine tasks. This was a complicated task with the authority structure of two lines: 1) Customs Quarantine Officer - Acting Chief Commissioner, Seoul - Acting Chief Commissioner, Seoul; 2) Superintendent - Dokpan. The actual quarantine of treaty port was implemented by Superintendent - Acting Chief Commissioner, Seoul. Matters of important decisions were accompanied by lower-level reports and higher-level instructions through the document administration procedure with the central government. The efficiency of this method was therefore limited whereas systematic administrative procedures were able to perform. This became the impetus that caused the third Chief Commissioner, Seoul, J. M. Brown to reform the framework of maritime affairs established in the Merrill period.