Förster Resonance Energy Transfer (FRET) microscopy is used in numerous biophysical and biomedical applications to monitor inter- and intramolecular interactions and conformational changes in the 2-10 nm range. FRET is currently being extended toin vivooptical imaging, its main application being in quantifying drug-target engagement or drug release in animal models of cancer using organic dye or nanoparticle-labeled probes. Herein, we compared FRET quantification using intensity-based FRET (sensitized emission FRET analysis using 3-cube IVIS imager) and macroscopic fluorescence lifetime (MFLI) FRET using a time-resolved ICCD system in small animal opticalin vivoimaging. The analytical expressions and experimental protocols required to quantify FRET efficiency 𝐸 and the fraction of donor molecules actually involved in FRET, 𝑓𝐷, are described in detail for both methodologies. Dynamicin vivoFRET quantification of transferrin receptor-transferrin binding was acquired in live intact nude mice upon intravenous injection of near infrared-labeled transferrin FRET pair and benchmarked againstin vitroFRET using hybridized oligonucleotides. Even though bothin vivoimaging techniques provided similar FRET quantification trends of receptor-ligand engagement, we demonstrate that MFLI FRET has significant advantages. Whereas the sensitized emission FRET approach using IVIS imager required 9 measurements (8 of which are used for calibration) acquired from three mice, MFLI FRET needed only one measurement collected from a single mouse. Hence, MFLI represents the method of choice for FRET measurements in intact, live mice to assess targeted drug delivery in longitudinal preclinical studies, as well as for many otherin vivobiomedical applications.