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Most evidence on son preference in Pakistan is reflected in the higher child mortality among females than males. The sex discrimination before birth is rarely reported in Pakistan. This is the first study to quantify prenatal sex discrimination in Pakistan on a subnational level. We provide annual estimates of the sex ratio at birth (SRB) from 1980 to 2020 and scenario-based projections of the number of missing female births up to 2050 by Pakistan province. The results are based on a comprehensive database consisting of 832,091 birth records from all available surveys and censuses. We adopted a Bayesian hierarchical time series model to synthesize different data sources. We identified Balochistan with an existing imbalanced SRB since 1980. For the rest provinces without past or ongoing SRB inflation, we projected the largest female birth deficit to occur in Punjab in 2033 under the scenario that the SRB transition process starts in 2021. We demonstrated important disparities in the occurrence and quantification of missing female births up to 2050.