Flexible piezoelectric energy harvesters have been regarded as an overarching candidate for achieving self-powered electronic systems for environmental sensors and biomedical devices using the self-sufficient electrical energy. In this research, we realize a flexible high-output and lead-free piezoelectric energy harvester by using the aerosol deposition method and the laser lift-off process. We also investigated the comprehensive biocompatibility of the lead-free piezoceramic device using ex-vivo ionic elusion and in vivo bioimplantation, as well as in vitro cell proliferation and histologic inspection. The fabricated LiNbO3-doped (K,Na)NbO3 (KNN) thin film-based flexible energy harvester exhibited an outstanding piezoresponse, and average output performance of an open-circuit voltage of ∼130 V and a short-circuit current of ∼1.3 μA under normal bending and release deformation, which is the best record among previously reported flexible lead-free piezoelectric energy harvesters. Although both the KNN and Pb(Zr,Ti)O3 (PZT) devices showed short-term biocompatibility in cellular and histological studies, excessive Pb toxic ions were eluted from the PZT in human serum and tap water. Moreover, the KNN-based flexible energy harvester was implanted into a porcine chest and generated up to ∼5 V and 700 nA from the heartbeat motion, comparable to the output of previously reported lead-based flexible energy harvesters. This work can compellingly serve to advance the development of piezoelectric energy harvesting for actual and practical biocompatible self-powered biomedical applications beyond restrictions of lead-based materials in long-term physiological and clinical aspects.