Background Urinary iodine is recommended by the world health organization as the main indicator to assess iodine status in a population. Despite this recommendation little is known about urinary iodine concentration in the study area. Therefore, this study aimed to determine the level of urinary iodine concentration among school-aged children. Methods An institution-based cross-sectional study design was used to assess the level of urinary iodine from April to June 2019 and a systematic random sampling technique was applied to select study participants. Socio-demographic characteristics were assessed using a pretested structured questionnaire and the laboratory method by Sandell–Kolthoff reaction method was used. Data were cleaned, coded, and entered into Epi data version 3.1 and then exported to SPSS version 21 software for analysis. Result A total of 634 study participants were enrolled in the study with a median age of 12 years (±SD = 2.0). The majority of the children were females (55.4%) and more than half of respondents report the use of iodized salt always. Median urinary iodine concentration was 158.5 μg/L (±SD = 104.1) with minimum and maximum values of 5.1 μg/L and 528.8 μg/L, respectively. The overall iodine deficiency in this study was 18.6% and severe deficiency constituted 7.4%. Conclusions The iodine deficiency of the school children aged 6 to 14 in the present study was 18.6% indicating high prevalence. A high proportion of iodine deficiency was observed among females and it increases as age increases. This indicates the need for an additional strategy to control iodine deficiency.