We perform a complete one-loop computation of the two-body flavour-changing top decays t → ch and t → cV (V = γ, Z), within the aligned two-Higgs-doublet model. We evaluate the impact of the model parameters on the associated branching ratios, taking into account constraints from flavour data and measurements of the Higgs properties. Assuming that the 125 GeV Higgs corresponds to the lightest CP-even scalar of the CP-conserving aligned two-Higgs-doublet model, we find that the rates for such flavour-changing top decays lie below the expected sensitivity of the future high-luminosity phase of the LHC. Measurements of the Higgs signal strength in the di-photon channel are found to play an important role in limiting the size of the t → ch decay rate when the charged scalar of the model is light.