Whale sharks (Rhincodon typus) are large filter-feeding species that have undergone major population declines due to anthropogenic threats, including fishing, climate change and ship strikes over the last century. Despite evidence of declines, it is often difficult to determine population sizes of whale sharks outside of genetics, however, age-structured demographic models can be used to calculate population sizes at present and in the past, overcoming this limitation. Using age-structured demographic modelling we estimate changes in whale shark populations over the last 125 years; coinciding with the expansion of steamships and the first records of whale shark fatalities due to ship strikes. Additionally, using the stable-age distributions from the Leslie Matrix models, we calculate the proportion of population sizes in each age class (i.e. juveniles or adults). Our models estimated that between 1897-2022, whale shark populations have declined by 1,071,428 individuals, resulting in an estimated global population of 375,143 whale sharks today, and of these, ~114,000 were classified as juveniles. Overall, our study identified an alternative approach to estimating the population sizes of whale sharks, highlighting substantial declines in population numbers. Collectively, these methods can be applied to other marine megafauna species, giving potential estimates of population sizes across their distribution.