In Malaysia, rare diseases affect fewer than 1 in 4,000 people. As of 2020, 491 rare diseases have been recorded in Malaysia, but with limited epidemiological data. As the first study in Malaysia, this retrospective cohort study examined the epidemiology and admission-related healthcare costs for adult rare disease patients in Langkawi. Among the 38 patients, rheumatological rare diseases topped the list (39.5%). The annual admission rate for rare diseases was 0.9%. Langkawi patients had lengthy hospital stays (9.7 days) and a 7.9% mortality rate. 23.7% of patients defaulted to follow-up, and 7.9% were referred to a tertiary hospital due to inadequate equipment or speciality care. Admission costs were Malaysian Ringgits (MYR) 244,598.63 (~US Dollars (USD) 51,280), with 80.2% from medication. The average healthcare resource utilisation was MYR 6,436.81/ patient/year (~USD 1,350/patient/year).