BackgroundPakistan has an inadequate vital event registration system, leading to fewer than half of all births being registered, and this issue is further exacerbated by systematic recall errors and omission of births. This study aims to evaluate direct and indirect methods of fertility estimation to analyze the trends and patterns of fertility rates in Pakistan from 1990 to 2018.Design/methodology/approachIndirect methods are utilized in this study to evaluate the direction and extent of changes in total and age-specific fertility rates, and these findings are compared to direct estimates. The study draws data on livebirths from four waves of the Pakistan Demographic and Health Survey that took place between 1990 and 2018. To ensure the quality of data, graphical methods and Whipple and Myers indices are employed. Additionally, the Brass Relational Gompertz model was used to analyze the data.ResultsThe Relational Gompertz model revealed that total fertility rates (TFRs) were higher than direct estimates by 0.4 children and age-specific fertility rates (ASFR) were higher for all age groups except the oldest. The difference was more significant among younger women aged 15–24, and less so for age groups 29 and above. The gap in estimated fertility between direct and indirect methods decreased with age.ConclusionThe indirect method is an invaluable tool in situations where direct measurement of fertility rates is challenging or impossible. By utilizing this method, policymakers can gain important insights into the fertility patterns and trends of a population, which is crucial for making informed decisions on fertility planning.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12905-023-02435-8.