Malawi is facing a rising chronic non-communicable disease (CNCD) epidemic. This study explored health seeking behaviour and related expenditure on CNCDs in rural Malawi, with specific focus on detecting potential differences across population groups. We used data from the first round of a panel household health survey conducted in rural Malawi between August and October 2012 on a sample of 1199 households. Multinomial logistic regression was used to analyse factors associated with health seeking choices for CNCDs, distinguishing between no care, informal care and formal care. Descriptive statistics (mean, standard deviation and median) were used to describe related household out-of-pocket expenditure. There were 475 individuals (equivalent to 8.4% of all respondents) reporting at least one CNCD. Among them, 37.3% did not seek any care, 42.5% sought formal care (facility-based care), and 20.2% opted for informal care (traditional or home treatment). Regression analysis showed that illness severity and duration, socio-economic status, being a household head, and the proportion of household members living with a CNCD were significantly associated with health care utilization. Among those seeking care, 65.8% incurred out-of-pocket expenditure with an average of USD 1.49 spent on medical treatment and an additional USD 0.50 spent on transport. Further qualitative inquiry is needed to understand the reasons for low service utilization and to explore the potential role of supply-side factors. To increase access to care for people suffering from CNCDs, the provision of a free Essential Health Package in Malawi ought to be strengthened through the integration of system-wide screening, risk factor modification and continuity of care options for people suffering from CNCDs. This would ensure affordable services to modulate health seeking behaviour of patients at risk of major chronic illnesses.