Purpose To assess the prevalence and factors associated with stunting and thinness among school-age children in rural primary schools in the East Dembia District, Northwest Ethiopia. Methods An institution-based cross-sectional study was conducted using a systematic random sampling procedure to select 840 school-aged children. A structured interviewer-administered questionnaire was used to collect the data. Height and weight measurements were taken, and a combined wet mount and concentration technique was used. Epi Data 3.1 was used to enter data, which was then exported to SPSS version 20 for analysis. Bi-variable and multivariable logistic regression analyses were done. Variables with a p-value of less than 0.05 were considered significantly associated with stunting and thinness. Results The prevalence of stunting and thinness was 25.5 and 13.0%, respectively. Being infected with an intestinal parasite (AOR =4.34; 95% CI: 2.52, 12.27), being in the age group 11–14 years (AOR =3.73; 95% CI: 2.19, 6.34), having the lowest dietary diversity practice (AOR =4.61; 95% CI: 1.73, 12.27), unimproved water sources (AOR =1.76; 95% CI: 1.07, 2.91), not practicing good hygiene practice (AOR =1.71; 95% CI: 1.04, 2.804) and having an unimproved latrine type (AOR =1.72; 95% CI: 1.03, 2.89) were significantly associated with stunting. On the other hand, unsecured food (AOR =1.74; 95% CI: 1.08, 2.81), eating less than 3 meals per day (AOR = 2.67; 95% CI: 1.11, 6.46), and untreated water (AOR =1.72; 95% CI: 1.08, 2.75) were factors associated significantly with thinness. Conclusion Stunting and thinness are predominant public health problems in the study area, provided that the prevalence of stunting is slightly higher than that of a national survey on health and nutrition in schoolchildren, whereas the prevalence of thinness is lower when compared to the same national survey. In this study, the primary factor that was significantly associated with stunting was dietary diversity; the primary factor that was associated with thinness was eating fewer than 3 meals per day. So, an integrated strategy is important to alleviate undernutrition among school-aged children in the current study area.