Summary Background and Aim To investigate and quantify the risks of AKI and ALI associated with remdesivir use, given the underlying diseases of SARS‐CoV‐2 infection. Methods This self‐controlled case series (SCCS) study was conducted using electronic hospital records between 23 January 2020 and 31 January 2021 as retrieved from the Hong Kong Hospital Authority which manages all laboratory‐confirmed COVID‐19 cases in Hong Kong. Outcomes of AKI and ALI were defined using the KDIGO Guideline and Asia Pacific Association of Study of Liver consensus guidelines. Incidence rate ratios (IRR) for AKI and ALI following the administration of remdesivir (exposure) in comparison to a non‐exposure period were estimated using the conditional Poisson regression models. Results Of 860 COVID‐19 patients administered remdesivir during hospitalisation, 334 (38.8%) and 137 (15.9%) had incident ALI and AKI, respectively. Compared with the baseline period, both ALI and AKI risks were increased significantly during the pre‐exposure period (ALI: IRR = 6.169, 95% CI = 4.549–8.365; AKI: IRR = 7.074, 95% CI = 3.763–13.298) and remained elevated during remdesivir treatment. Compared to the pre‐exposure period, risks of ALI and AKI were not significantly higher in the first 2 days of remdesivir initiation (ALI: IRR = 1.261, 95% CI = 0.915–1.737; AKI: IRR = 1.261, 95% CI = 0.889–1.789) and between days 2 and 5 of remdesivir treatment (ALI: IRR = 1.087, 95% CI = 0.793–1.489; AKI: IRR = 1.152, 95% CI = 0.821–1.616). Conclusion The increased risks of AKI and ALI associated with intravenous remdesivir treatment for COVID‐19 may be due to the underlying SARS‐CoV‐2 infection. The risks of AKI and ALI were elevated in the pre‐exposure period, yet no such increased risks were observed following remdesivir initiation when compared to the pre‐exposure period.