Background Poor quality of pediatric healthcare services at health facilities is a major contributing factor to child morbidity and mortality in low- and middle-income countries, including Ethiopia, and it brings parental dissatisfaction. Eliciting parents’ perception is an important method used to assess functionality or quality of pediatric healthcare services. Thus, the objective of this study was to assess the perceived quality of pediatric healthcare services and to identify factors for it in Felege-Hiwot Comprehensive Specialized Hospital, Northwest Ethiopia. Methods A facility-based cross-sectional study was conducted among parents of childhood patients from September 15, 2019 to October 15, 2019; 407 participants were recruited. Stratified random sampling was used to select respondents and data were collected using face-to-face interviews. Frequencies, percentages, and means with standard deviations were used to describe profiles of respondents. Both bi-variable and multivariable logistic regressions were used to model the odds of perceived quality of pediatric healthcare services. Results The proportion of perceived quality of pediatric healthcare services was 57.6% (95% CI:52.6–62.3%). College and above parental education status (AOR=5.22, 95% CI:2.39–11.38), urban residency (AOR=3.35, 95% CI:1.97–5.72), outpatient services (AOR=2.52, 95% CI:1.35–4.71), and surgical illnesses (AOR=2.18, 95% CI:1.28–3.73) were independent determinants for increased parental lower perceived level of quality. The odd of parental lower perceived level of quality was 2.42-times greater in those parents who did not prefer the hospital for revisiting (AOR=2.42, 95% CI:1.36–4.30). Conclusion Perceived quality of healthcare services in the hospital was low compared to the national plan which reflected that childhood patients did not receive optimal care. Educational status, place of residence, service delivering unit, illness type, and intention of hospital preference were independent determinants for parental perceived quality of pediatric healthcare service delivery. Continuous and periodic parental feedback should be considered in order to assess their satisfaction which in turn is an insight for quality improvement to be taken by the facility managers.