African schoolchildren's dietary habits are likely changing in the realm of the nutrition transition, particularly in urban areas, but data on their diet and on determinants are scanty. In order to design relevant interventions for this priority target group, the study aimed to assess food habits and their determinants in schoolchildren of Ouagadougou. In a cross-sectional survey, fifth-grade schoolchildren filled during school hours a questionnaire to assess consumption frequency of 'healthy' foods (fruits, vegetables, meat, fish, legumes) and 'unhealthy' (superfluous) items (cake, cookies, candies, ice, soda) and underlying factors, using Green's PRECEDE model. The study included 769 schoolchildren, mean age 11.7 ± 1.4 years, from eight public and four private schools. Consumption scores of unhealthy items were significantly higher than healthy foods (p = 0.001). During the week prior to the survey, 25% of children had eaten no fruit, 20% no meat, 20% no legumes, 17% no fish and 17% no vegetables. While less than 4% ate fruits or vegetables every day, 18.3% ate ice pop every day. Children eating cookies, cakes and candy every day were up to seven-fold those eating fruits, vegetables or legumes. Compared to public-school pupils, those from private schools consumed both healthy and unhealthy items more frequently (p = 0.002 and p = 0.007, respectively). Urban schoolchildren had significantly higher unhealthy food scores (p = 0.027) compared to peri-urban schools. Children's healthy and unhealthy food consumption was primarily explained by perceived decisional power and availability [facilitating factors] for both types of foods, and maternal reinforcement for healthy foods and peers' reinforcement for consumption of unhealthy items. Overall, facilitating factors rated higher for unhealthy than healthy foods. The study showed that city schoolchildren's eating behaviours are far from optimal. Nutrition interventions should be tailored to address the underlying factors in order to impact on behaviours, thereby preventing both dietary inadequacies and excess.