Background: Globally, menstrual hygiene is an important public health problem but disproportionally high poor practice of menstrual hygiene in developing countries including Ethiopia. More than half of Ethiopian schoolgirls missed their class during the menstrual period due to poor menstrual hygiene practice. However, there is limited information on the level of menstrual hygiene practice by the residence and the reasons for the variation. Objectives: Assess menstrual hygiene practice and its associated factors among schoolgirls in North Wollo Zone, Northeast Ethiopia, 2020 Methods: An institution-based comparative cross-sectional study was employed from February 30 to March 13, 2020 among 1078 schoolgirls (539 urban and 539 rural) by using multi-stage sampling techniques. Data were collected by self -administered questionnaire and observational checklist. The data were entered into epi-info version7 and further analyzed using SPSS version 23. A bivariable and multivariable binary logistic regression analysis with a 95% confidence interval were employed. A P-value of < 0.05 was considered statistically significant. Results: This study revealed that the overall magnitude of good menstrual hygiene practice was 52.9% with (95%CI: 50%-56%) and the magnitude of good menstrual hygiene practice among urban and rural schoolgirls was 65.9% (95% CI: 62%-70%) and 39.9% (95% CI: 36%- 44%) with p<0.001 respectively. Aged below 18 years old (AOR=1.58, 95%CI: 1.05- 2.39), learning about menstrual hygiene (AOR=1.89, 95%CI: 1.21- 2.97), hearing about menstrual hygiene (AOR=4.98, 95%CI: 2.71- 9.13) and discussing menstrual hygiene (AOR=2.56, 95%CI: 1.25- 5.27) were factors associated with good menstrual hygiene practice among urban schoolgirls. Whereas, good knowledge on menstrual hygiene (AOR=5.47, 95%CI: 3.68- 8.12), learning about menstrual hygiene (AOR=1.75, 95%CI: 1.13- 2.70) and hearing about menstrual hygiene (AOR=3.34, 95%CI: 1.44-7.76) were positively associated with good menstrual hygiene practice among rural schoolgirls. Conclusion and recommendation: Only seven and four in every ten urban and rural schoolgirls had good menstrual hygiene practice respectively. It was higher among urban schoolgirls than rural schoolgirls. Hearing about menstrual hygiene before menarche and have been learned about menstrual hygiene in the school at both areas were significant factors associated with good menstrual hygiene practice. Therefore, educating girls about menstrual hygiene and open discussion on menstrual hygiene should be strengthened. Encourage the families and schools to inform their children about menstrual hygiene before menarche happens. Keywords: Menstrual hygiene, schoolgirl, North Wollo, Ethiopia