The recent discovery of higher-order topological insulators (HOTIs) has significantly extended our understanding of topological phases of matter. Here, we predict that second-order corner states can emerge in the dipolar-coupled dynamics of topological spin textures in two-dimensional artificial crystals. Taking a breathing honeycomb lattice of magnetic vortices as an example, we derive the full phase diagram of collective vortex gyrations and identify three types of corner states that have not been discovered before. We show that the topological zero-energy corner modes are protected by a generalized chiral symmetry in the sexpartite lattice, leading to particular robustness against disorder and defects, although the conventional chiral symmetry of bipartite lattices is absent. We propose the use of the quantized $mathbb{Z}_{6}$ Berry phase to characterize the nontrivial topology. Interestingly, we observe corner states at either obtuse-angled or acute-angled corners, depending on whether the lattice boundary has an armchair or zigzag shape. Full micromagnetic simulations confirm the theoretical predictions with good agreement. Experimentally, we suggest using the recently developed ultrafast Lorentz microscopy technique [M{o}ller emph{et al}.,{arXiv:1907.04608}] to detect the topological corner states by tracking the nanometer-scale vortex orbits in a time-resolved manner. Our findings open up a promising route for realizing higher-order topologically protected corner states in magnetic systems and finally achieving topological spintronic memory and computing.