Woman scientists have for long been under-represented as recipients of academic prizes. The reasons for this lack of recognition are manifold, including potential gender bias amongst award panels and nomination practices. This dataset of the gender distribution of 8747 recipients of 345 scientific medals and prizes awarded by 11 General Scientific Societies as well as subject-specific societies in the Earth and Environmental Sciences and in Cardiology between 1731 and 2021 explores the magnitude, temporal trends and potential drivers of observed gender imbalances. Our analysis revealed women were particularly underrepresented in awards named after men with awards not named after a person or named after a woman being more frequently awarded to woman scientists. Time-series analysis confirmed persisting trends that are only starting to change since the early 2000s, indicating that a lot remains to be accomplished to achieve true equity. We encourage the scientific community to extend our data and analysis, as they represent important evidence of the recognition of academic achievements towards other under-represented groups and including also nomination information. Dataset: All primary data underlying this publication are available at https://osf.io/ynbzm/. Dataset License: License under which the dataset is made available: CC-BY.