Malnutrition is a matter of public concern worldwide, and remains the greatest challenge in Sub-Saharan Africa. The literature shows that, malnutrition is one of the major causes of childhood deaths and developmental problems around the globe. This study analyzed the factors affecting stunting and wasting in children 0-59 month's old in Northern Ghana using secondary data from Feed the Future Northern Ghana survey data. The study found that the prevalence rate of stunting was 37.14%, 35.79%, and 25.11% for the Northern, Upper East and Upper West regions respectively, while the prevalence of wasting was found to be 11.11%, 11.24%, and 7.31% for these regions. The study also found that the age of child, household total expenditure, region, age of the head of household and household access to safe drinking water were found to be significantly associated with both stunting and wasting. Furthermore, the gender of child, and household location in an urban area, were also found to be significantly associated with only stunting while household access to productive capital was also found to be significantly associated with only wasting. In conclusion, these factors identified should be taken into account when designing interventions on malnutrition in Northern Ghana.