Uranium holds significant global importance due to its crucial role in the energy generation sector. Uranium is present in the Earth’s crust with ~1–3 ppm. Furthermore, high concentration is also found in the sediments having rich organic matter content. The average values of uranium in phosphorite, shale, sandstone, and carbonate are 120, 3.5, 0.5, and 2.2 ppm, respectively. The main endeavor of the current work is to discuss the uranium geochemistry of phosphorites of Masrana and Kimoi blocks of Mussoorie syncline to understand the concentration and behavior of uranium with respect to other elements in these phosphorites. The studied phosphorites show dull gray to brown-black color and are hosted by black shale, chert, and minor carbonate rocks of Neoproterozoic to Early Cambrian age, which belong to the lowermost sequence of the Tal Group of the Lesser Himalaya. These phosphorites are rarely bedded and display incrustations of white and orange color. Nodular phosphorite is found in black shales that lie in contact with the phosphorite horizon. Nodules show mostly spheroidal, flattened, plano-convex, and ellipsoidal shapes. Alternate bands of carbonate and phosphate minerals, having a thickness in mm, are seen in laminated phosphorites. In this variety of phosphorites, the phosphatic layer is made of collophane and this class retains the maximum concentration of phosphate than that of other classes. The studied samples are rich in CaO, P2O5, SiO2, Al2O3, Fe2O3, K2O, V, Cr, Zn, Sr, Zr, Nb, and Ba but depleted in MgO, MnO, and TiO2. The uranium content in the studied samples varies from 1.37 to 37.5 ppm with an average of 16.7 ppm. The negative correlation of U with P2O5 suggests the removal of uranium from the atomic structure of apatite and substitution of P5+, while the inverse correlation between U and CaO suggests mutual replacement of Ca2+ by U4+ in the apatite crystal structure. Thus, the removal of U from the crystal lattice is responsible for the low contents of U in these phosphorites. The sympathetic/weak positive relationship of U with K2O indicates partial replacement of Ca2+ by K+ in the apatite atomic structure, which infers the alkaline conditions of the basin of deposition during phosphatization. The positive correlation of U with Ni, Cu, Zn, and Co and the weak negative relation of U with V and Cr, suggest that the phosphate-bearing rocks are deposited under sulfur-reducing/euxinic conditions. Additionally, Ni, Cu, Zn, and Ba are the tracers for the abundance of organic matter (OM), i.e., they are incorporated into the sediments primarily in association with OM. A higher concentration of Ni and Cu suggests (i) a high influx of OM released these elements from the surroundings and concentrated them in the sediments, and (ii) a reducing environment enabled the sedimentary fixation of Ni and Cu. The positive correlation of U with these elements suggests a similar process for U enrichment in the studied phosphate-bearing rocks.