Context. The progenitors of many core-collapse supernovae (CCSNe) are expected to be in binary systems. After the SN explosion in a binary, the companion star may suffer from mass stripping and be shock heated as a result of the impact of the SN ejecta. If the binary system is disrupted by the SN explosion, the companion star is ejected as a runaway star, and in some cases as a hypervelocity star. Aims. By performing a series of three-dimensional (3D) hydrodynamical simulations of the collision of SN ejecta with the companion star, we investigate how CCSN explosions affect their binary companion. Methods. We use the BEC stellar evolution code to construct the detailed companion structure at the moment of SN explosion. The impact of the SN blast wave on the companion star is followed by means of 3D smoothed particle hydrodynamics (SPH) simulations using the Stellar GADGET code. Results. For main-sequence (MS) companion stars, we find that the amount of removed stellar mass, the resulting impact velocity, and the chemical contamination of the companion that results from the impact of the SN ejecta strongly increases with decreasing binary separation and increasing explosion energy. Their relationship can be approximately fitted by power laws, which is consistent with the results obtained from impact simulations of Type Ia SNe. However, we find that the impact velocity is sensitive to the momentum profile of the outer SN ejecta and, in fact, may decrease with increasing ejecta mass, depending on the modeling of the ejecta. Because most companion stars to Type Ib/c CCSNe are in their MS phase at the moment of the explosion, combined with the strongly decaying impact effects with increasing binary separation, we argue that the majority of these SNe lead to inefficient mass stripping and shock heating of the companion star following the impact of the ejecta. Conclusions. Our simulations show that the impact effects of Type Ib/c SN ejecta on the structure of MS companion stars, and thus their long-term post-explosion evolution, is in general not dramatic. We find that at most 10% of their mass is lost and their resulting impact velocities are less than 100 km s −1 .