Patient organisations play an increasingly crucial role in the pharmaceutical sector, yet their impact on innovation remains unexplored. We estimate the impact of patient organisations on R&D activity in the context of rare diseases in Europe using a proprietary dataset that maps clinical trials from discovery to phase III across 29 countries, 1893 indications, and 30 years (1990–2019). By applying difference-in-differences and event study methodologies to a panel of 1,646,910 unique R&D observations, we find that country-indication pairs with at least one operating patient organisation have a higher rate of R&D activity compared to those without, with stronger effect in more prevalent rare diseases compared to ultra-rare conditions. We observe a lag in effects from patient organisation introduction, suggesting it takes approximately five years for these organisations to affect R&D activity. Overall, our work suggests that patient organisations play an important role in steering R&D efforts in rare diseases. Further research is needed to better understand mechanisms driving this effect and the potential impact of patient organisations on existing health inequities.