Human mobility is undisputedly one of the critical factors in infectious disease dynamics. Until a few years ago, researchers had to rely on static data to model human mobility, which was then combined with a transmission model of a particular disease resulting in an epidemiological model. Recent works have consistently been showing that substituting the static mobility data with mobile phone data leads to significantly more accurate models. While prior studies have exclusively relied on a mobile network operator’s subscribers' aggregated data, it may be preferable to contemplate aggregated mobility data of infected individuals only. Clearly, naively linking mobile phone data with infected individuals would massively intrude privacy. This research aims to develop a solution that reports the aggregated mobile phone location data of infected individuals while still maintaining compliance with privacy expectations. To achieve privacy, we use homomorphic encryption, zero-knowledge proof techniques, and differential privacy. Our protocol’s open-source implementation can process eight million subscribers in one and a half hours. Additionally, we provide a legal analysis of our solution with regards to the EU General Data Protection Regulation.