Time‐correlated single photon counting is the “gold‐standard” method for fluorescence lifetime measurements and has demonstrated potential for clinical deployment. However, the translation of the technology into clinic is hindered by the use of ultrasensitive detectors, which make the fluorescence acquisition impractical with bright lighting conditions such as in clinical settings. We address this limitation by interleaving periodic fluorescence detection with synchronous out‐of‐phase externally modulated light source, thus guaranteeing specimen illumination and a fluorescence signal free from bright background light upon temporal separation. Fluorescence lifetime maps are generated in real‐time from single‐point measurements by tracking a reference beam and using the phasor approach. We demonstrate the feasibility and practicality of this technique in a number of biological specimens, including real‐time mapping of degraded articular cartilage. This method is compatible and can be integrated with existing clinical microscopic, endoscopic and robotic modalities, thus offering a new pathway towards label‐free diagnostics and surgical guidance in a number of clinical applications.