Highly intense NIR emissions in the first and second biological windows and a remarkable UV–Vis and NIR to NIR energy conversion were observed for Pr3+, Yb3+ co-doped yttria nanoparticles, synthesized via the homogeneous precipitation method. A single-phase body center cubic Y2O3 structure was formed for all the samples after annealing 900 °C for 2 h. Increasing the dopants content, from 0.5 to 5.0 mol %, the replacement of Y3+ by Pr3+ and Yb3+ ions lead to a lattice expansion, which could be calculated. Spherical monodispersed nanoparticles, constituted of several crystallites, were observed by TEM and SEM images. The particles size ranged from 143 to 272 nm for the as-prepared samples and from 88 to 202 nm for the samples annealed at 900 °C. The crystallite size was estimated by Debye-Scherrer and Williamson-Hall methods and ranged from 6 to 27 nm with an average of 13 nm. Photoluminescent studies evidenced pronounced Pr3+ and Yb3+ near infrared (NIR) emission under ultraviolet, visible, and NIR excitation. How the Yb3+ ions co-doping, as well as, the total rare earth content, affected the luminescence properties, were evaluated, along with the energy transfer process involving UV–Vis and NIR to NIR energy conversion between the doping ions and the host. The energy was transferred between the Y2O3 host and Pr3+, Yb3+ upon CT band excitation at 290 nm. NIR emission at 948, 1080, 1115 nm, and 1.5 μm attributed to the Pr3+ transitions 3P0,1→1G4, 1D2→3F3, 1D2→3F4, and 1D2→1G4, denoting the 1D2 population through a multiphonon relaxation process (3P0+3H4→3H6+1D2). A concentration quenching process was ascertained in the highest concentration of dopants (5.0 mol % in total), which indicated that cross-relaxation took place. Both the Yb3+-doped and Pr3+, Yb3+ co-doped samples presented the Yb3+ emission 2F5/2→2F7/2 at 976 nm. All the structural, morphological, and spectroscopic properties of the materials make these spherical yttria nanoparticles potential NIR emitting probes candidates for advances in biophotonics, especially for deep-tissue imaging using NIR I and NIR II biological windows.