Background Rural and urban populations have disparate socio-demographic and economic characteristics, which have an influence on equity and their health seeking behavior. We examined and compared the health care seeking behavior for perceived morbidity between urban and rural households in Southwest Ethiopia. Methods Analytic cross-sectional study was conducted among urban and rural households living in Esera district of Southwest Ethiopia. A random sample of 388 head of households (126 urban and 262 rural)were selected. A pretested and structured questionnairewas used for data collection with face-to-face interview. In addition to descriptive methods, binary logistic regression was used to identify factors associated with health seeking behavior at p value of less than 0.05. Results Of the sample household heads, 377 (97.2%) (119 urban and 258 rural)were successfully interviewed. Among these, 58.4% (95% CI, 53.3'63.3%) of the households sought care from modern health care that was lower among rural (48.1%) than urban (80.7%) households. The prevalence of self-treatmentwas 35.3% in urban and 46.1% in rural households. Among the factors considered for modern health care utilization, higher monthly income (AOR, 5.6; 95% CI, 2.04'15.4), perceived severity of disease (AOR, 2.5; 95% CI, 1.1'5.8), acute duration of disease (AOR, 8.9; 95% CI, 2.4'33.3) and short distance from health facilities (AOR, 3; 95% CI, 1.2'8.4) among rural and being married (AOR, 11.3; 95% CI, 1.2' 110.2) and perceived severity of disease (AOR, 6.6; 95% CI, 1.1'10.9) among urban households showed statistically significant association. Conclusions The general health seeking behavior of households on perceived morbidity was satisfactory but lower in rural compared to urban households. Self-medicationwas also widely practiced in the study area. The findings signal the need to work more on accessibility and promotion of healthcare seeking behavior especially among rural households.