Background Influenza is a contagious respiratory illness that can cause life-threatening complications among high-risk groups. Estimating the economic burden of influenza is essential to guide policy-making on influenza vaccination programmes, especially in resource-limited settings. This study aimed to estimate the economic burden of influenza on older adults (those aged 60 years) in Malaysia from the provider’s perspective. Methods The main data source in this study was the MY-DRG Casemix database of a teaching hospital in Malaysia. Cases with principal and secondary diagnoses coded in the International Classification of Diseases version 10 (ICD-10) as J09, J10.0, J10.1, J10.8, J11.0, J11.1, J11.8, J12.8, and J12.9, which represent influenza and its complications, were included in the study. The direct cost of influenza at all severity levels was calculated from the casemix data and guided by a clinical pathway developed by experts. The effect of the variations in costs and incidence rate of influenza for both the casemix and clinical pathway costing approaches was assessed with sensitivity analysis. Results A total of 1,599 inpatient and 407 outpatient influenza cases were identified from the MYDRG Casemix database. Most hospitalised cases were aged <18 years (90.6%), while 77 cases (4.8%) involved older people. Mild, moderate, and severe cases comprised 56.5%, 35.1%, and 8.4% of cases, respectively. The estimated average annual direct costs for managing mild, moderate, and severe influenza were RM2,435 (USD579), RM6,504 (USD1,549), and RM13,282 (USD3,163), respectively. The estimated total annual economic burden of influenza on older adults in Malaysia was RM3.28 billion (USD782 million), which was equivalent to 10.7% of the Ministry of Health Malaysia budget for 2020. The sensitivity analysis indicated that the influenza incidence rate and cost of managing severe influenza were the most important factors influencing the total economic burden. Conclusions Overall, our results demonstrated that influenza imposes a substantial economic burden on the older Malaysian population. The high cost of influenza suggested that further efforts are required to implement a preventive programme, such as immunisation for older people, to reduce the disease and economic burdens.