Background: Antimicrobial resistance (AMR) poses a significant threat to global health and economic development. In Malawi, the economic costs associated with AMR remain largely unknown which may hinder resource allocation and policy prioritization. Method: The study used instrumental variable 2-stage least squares regression to analyze patient level cost data at tertiary and secondary level facilities primarily collected from 610 patients with urinary tract infection (UTI) or blood stream infection (BSI) using a questionnaire. Results: Findings indicate that E. coli (43%) followed by K. pneumoniae (14%), and S. aureus (10%) were common pathogens overall. UTI was common (51%) compared to BSI (49%) yet BSI had a higher average cost than UTI for both susceptible and resistant patient categories. In terms of costs, a patient spent MK283,815.10 (US$163.71) on average as a result of AMR infection. The total cost reached as high as MK13,500,000 (US$7,786.90). Patients with a resistant infection incurred, on average MK161,785 (US$93.32) more than patients whose infection was susceptible, with the additional costs being driven by prolonged hospitalization among other factors. The direct medical costs averaged MK37,165.29 (US\(21.44) while direct non-medical costs averaged MK61,908.71 (US\)35.71). Productivity losses for the patient and guardian(s) were a major cost averaging MK160,322.80 (US$92.49). The regression results further showed that having a bank account as a proxy of wealth, non-farm business, longer travel duration, BSI, and K. pneumoniae as causing pathogens were significantly associated with increased cost burden among the patients. Conclusions: AMR imposes substantial economic burden on Malawi's health system, with most costs falling on patients. Further strengthening of AMR surveillance and stewardship are needed as critical elements of Malawi’s National Action Plan. However, measures should also be taken to mitigate the economic consequences related to AMR, especially for patients who bear the brunt of these costs for lack of financial protection in Malawi’s health system.