Hyperfine splittings play an important role in quantum information and spintronics applications. They allow for the readout of the spin qubits, while at the same time providing the dominant mechanism for the detrimental spin decoherence. Their exact knowledge is thus of prior relevance. In this work, we analytically investigate the relativistic effects on the hyperfine splittings of hydrogen-like atoms, including finite-size effects of the nucleis’ structure. We start from exact solutions of Dirac’s equation using different nuclear models, where the nucleus is approximated by (i) a point charge (Coulomb potential), (ii) a homogeneously charged full sphere, and (iii) a homogeneously charged spherical shell. Equivalent modelling has been done for the distribution of the nuclear magnetic moment. For the 1s ground state and 2s excited state of the one-electron systems H1, H2, H3, and He+3, the calculated finite-size related hyperfine shifts are quite similar for the different structure models and in excellent agreement with those estimated by comparing QED and experiment. This holds also in a simplified approach where relativistic wave functions from a Coulomb potential combined with spherical-shell distributed nuclear magnetic moments promises an improved treatment without the need for an explicit solution of Dirac’s equation within the nuclear core. Larger differences between different nuclear structure models are found in the case of the anisotropic 2p3/2 orbitals of hydrogen, rendering these excited states as promising reference systems for exploring the proton structure.