Malnutrition remains a public health issue among children in resource poor countries where seasonality affects food availability, food consumption, and nutritional status of a population. The aim of this study was to determine prevalence of anemia, low vitamin A and associated factors in school-age children in dry and wet season in a peri-urban setting. This was a six months observational study where data and samples were collected from school age children 6–12 years in mid-March (dry season) and mid-August (rainy season) 2020. Data and biological samples collected, were analyzed to determine prevalence of adequate dietary intakes, anemia, low vitamin A, and under-nutrition among participants. The study participants had 40.9% and 32.3% prevalence of anemia, 30.1% and 19.4% prevalence of low vitamin A, 12.9% and 10.8% level of wasting, and 63.4% and 94.6% level of adequate iron intake in the dry and wet seasons respectively. The cohort of anemic participants had mean hemoglobin concentrations as 10.6(1.7)ug/dl and 11.4(91.1)ug/dl in the dry and wet seasons respectively and significantly different at p = 0.001. The prevalence of anemia among them declined from 100.0% in the dry season to 79.0% in the wet season. They had mean serum retinol concentration as 22.4(6.4)ug/dl and 25.0(8.9)ug/dl, (significantly different at p = 0.014), prevalence of low vitamin A at 36.8% and 31.6%, prevalence of wasting as 23.7% and 18.4%, and prevalence of thinness as 10.2% and 7.9% in the dry and wet seasons respectively. Anemia associated significantly with parental monthly income of 1000–1500 cedis (180–269 USD), (OR:046, p = 0.039), and low vitamin A level (<20 μg/dl), (OR: 0.319, p = 0.049) in the dry season. Anemia associated significantly with low serum retinol (<20 μg/dl) (OR:0.070, p = 0.003) and dry season’s low hemoglobin (<11.5 g/dl) (OR:0.302, p = 0.034) among the participants. Seasonal variation from the dry to wet season have consequential effect on anemia, and nutritional status with associated factors among the study participants. Anemia associated significantly with parental monthly income in the dry season and with low serum retinol and dry season’s low hemoglobin in the wet season. Nutrition interventions will be more beneficial to the study participants during the dry season.