Background Childhood epilepsy is a major public health problem worldwide. Even though anti-seizure medications (ASM) have been demonstrated to control seizures, children with epilepsy continue to have frequent seizures. There is a scarcity of data on seizure control status among pediatric epileptic patients in Ethiopia. The aim of this study was to assess seizure control status and associated factors among pediatric epileptic patients. Methods A hospital based cross-sectional study was done on 261 pediatric epileptic patients being followed up at the University of Gondar Comprehensive and Specialized Hospital, Northwest Ethiopia, from May 11 to August 11, 2019. The data were collected through caregiver interviews and patients’ medical records. All independent variables with p value of ≤ 0.2 in univariate analysis were taken to multivariable analysis. Adjusted odds ratio (AOR) with a 95% confidence interval was computed to see the predictors of seizure control status. Level of statistical significance was declared if p-value < 0.05. Result From a total of 261 patients, 159 (60.9%) were males and had a mean age was 10.16 ± 4.62 years. More than half (57.1%) of participants were urban dwellers. Almost all (98.5%) were diagnosed with generalized tonic-clonic seizures. Majority (75.1%) of the patients were on mono-therapy. Forty-six (17.6%) of the patients reported adverse effects related to ASMs. Two hundred-three (77.8%) of the patients were adherent to their medications. Nearly half (49.0%) of the patients had controlled seizures. Urban residency (AOR: 2.12; 95% CI: 1.15–3.89; P = 0.016), adherence to medication (AOR: 3.92; 95% CI: 1.84–8.36; P < 0.001), use of combined ASM(AOR: 0.29; 95% CI: 0.14–0.59; P = 0. 001), durations of ASM use [2–5 years (AOR: 5.81; 95% CI: 2.89–11.70; P <0.001) and >5years (AOR: 4.80; 95% CI: 1.91–12.09; P = 0.001)]were significantly associated with seizure control status. Conclusion Inadequate numbers of pediatric epileptic patients’ at the Ethiopian neurologic clinic achieved seizure control. Coming from a rural area, non-adherence to ASMs, use of multiple ASMs, and the use of ASMs for <2years were found to have a significant association with poorer seizure control, needing special attention to get control of seizure. Caregivers should closely monitor and address any barriers that contribute to ASM non-adherence and adverse drug events.