Background: Ethiopia is the second most populous nation in Africa. Family planning is a viable solution to control such fast growing population. It is believed that population growth and family planning health facilities are closely related concepts. This study aimed to examine the number of modern contraceptive users over time at health facilities using generalized linear mixed model. Methodology: In this study, the data source was PMA2020 project with a total of 382 health facilities which can deliver family planning services. The study analysed the number of modern contraceptive users per a month in the health facilities within 6 months’ interval. Mean profile plots, variance profile plots, univariate analysis and multivariable analysis was employed. Generalized linear mixed model with negative binomial distribution was used. Results: Results show that the mean number of modern contraceptive users increased over time. In addition, number of modern contraceptive users depends on type of health facility, region, resident, availability of community health volunteers, stock out experience, number of opening days/week of the facility and external supervision. Conclusions: The study found that from the main effects, visiting times, type of health facility, region and community health volunteers were significantly affected the average numbers of contraceptive users in the study area. On the other hand, from the interaction effects, time * stock out experience, facility type * region, facility type *residence area, facility type *number of opening days per a week were identified as significant predictors for the progression of number of modern contraceptive users. Moreover, on average number of modern contraceptive users increased over time