Background Despite a free access to public health services policy in most sub-Saharan African countries, households still contribute to total health expenditures through out-of-pocket expenditures. This reliance on out-of-pocket expenditures places households at a risk of catastrophic health expenditures and impoverishment. This study examined the incidence of catastrophic health expenditures, impoverishing effects of out-of-pocket expenditures on households and factors associated with catastrophic expenditures in Malawi. Methods We conducted a secondary analysis of the most recent nationally representative integrated household survey conducted by the National Statistical Office between April 2016 to 2017 in Malawi with a sample size of 12447 households. Catastrophic health expenditures were estimated based on household annual nonfood expenditures and total household annual expenditures. We estimated incidence of catastrophic health expenditures as the proportion of households whose out-of-pocket expenditures exceed 40% threshold level of non-food expenditures and 10% of total annual expenditures. Impoverishing effect of out-of-pocket health expenditures on households was estimated as the difference between poverty head count before and after accounting for household health payments. We used a multilevel binary logistic regression model to assess factors associated with catastrophic health expenditures. Results A total of 167 households (1.37%) incurred catastrophic health expenditures. These households on average spend over 52% of household nonfood expenditures on health care. 1.6% of Malawians are impoverished due to out-of-pocket health expenditures. Visiting a religious health facility (AOR = 2.27,95% CI:1.24-4.15), hospitalization (AOR = 6.03,95% CI:4.08-8.90), larger household size (AOR = 1.20,95% CI:1.24-1.34), higher socioeconomic status (AOR = 2.94,95% CI:1.39-6.19), living in central region (AOR = 3.54,95% CI:1.79-6.97) and rural areas (AOR = 5.13,95% CI:2.14-12.29) increased the odds of incurring catastrophic expenditures. Conclusion The risk of catastrophic health expenditures and impoverishment persists in Malawi. This calls for government to improve the challenges faced by the free public health services and design better prepayment mechanisms to protect more vulnerable groups of the population from the burden of out-of-pocket payments.