The aim of this review is to present the state-of-the art achievements reported in the last two decades in the field of pulsed laser deposition (PLD) of biocompatible calcium phosphate (CaP)-based coatings for medical implants, with an emphasis on their in vivo biological performances. There are studies in the dedicated literature on the in vivo testing of CaP-based coatings (especially hydroxyapatite, HA) synthesized by many physical vapor deposition methods, but only a few of them addressed the PLD technique. Therefore, a brief description of the PLD technique, along with some information on the currently used substrates for the synthesis of CaP-based structures, and a short presentation of the advantages of using various animal and human implant models will be provided. For an in-depth in vivo assessment of both synthetic and biological-derived CaP-based PLD coatings, a special attention will be dedicated to the results obtained by standardized and micro-radiographies, (micro) computed tomography and histomorphometry, tomodensitometry, histology, scanning and transmission electron microscopies, and mechanical testing. One main specific result of the in vivo analyzed studies is related to the demonstrated superior osseointegration characteristics of the metallic (generally Ti) implants functionalized with CaP-based coatings when compared to simple (control) Ti ones, which are considered as the “gold standard” for implantological applications. Thus, all such important in vivo outcomes were gathered, compiled and thoroughly discussed both to clearly understand the current status of this research domain, and to be able to advance perspectives of these synthetic and biological-derived CaP coatings for future clinical applications.