Hand, foot, and mouth disease (HFMD) is a common viral communicable disease in Malaysia, characterized by its self-limiting nature, yet it leads to numerous outbreaks and fatalities, particularly among young children. The current study aimed to determine the prevalence, geographic distribution, temporal patterns, and associated factors of HFMD cases within the Bachok District of Kelantan, spanning the years 2018 to 2022. A retrospective cohort study analysed extract data on independent factors and notification status from the Communicable Disease Control Information System (CDCIS). Simple and multiple logistic regression analyses were employed on a cohort of 1351 HFMD’s notifications. The retrospective analysis reveals a predominant HFMD’s notification were males (56.7%). Outpatient care was common (98.4%), with primary health care being the main choice. Logistic regression indicates higher odds for HFMD in those attending primary health care or private practitioners, daycare attendees, during the Southwest Monsoon season, and before the Movement Control Order (MCO) implementation, emphasizing key risk factors for HFMD. This study’s integrative approach recognizes that health and disease are often influenced by a combination of factors spanning the ecological, biological, and clinical domains. Thus, emphasizing the need for a comprehensive understanding when formulating public health strategies particularly in primary healthcare settings and daycare facilities during the Southwest Monsoon season.