Dirac and Weyl fermions appear as quasiparticle excitations in many different condensed-matter systems. They display various quantum transitions which represent unconventional universality classes related to the variants of the Gross-Neveu model. In this paper we study the bosonized version of the standard Gross-Neveu model—the Gross-Neveu-Yukawa theory—at three-loop order, and compute critical exponents in dimensions for a general number of fermion flavors. Our results fully encompass the previously known two-loop calculations, and agree with the known three-loop results in the purely bosonic limit of the theory. We also find the exponents to satisfy the emergent superscaling relations in the limit of a single-component fermion, order by order up to three loops. Finally, we apply the computed series for the exponents and their Padé approximants to several phase transitions of current interest: metal-insulator transitions of spin-1/2 and spinless fermions on the honeycomb lattice, emergent supersymmetric surface field theory in topological phases, as well as the disorder-induced quantum transition in Weyl semimetals. Comparison with the results of other analytical and numerical methods is discussed.