We study second-order topological insulators and semimetals characterized by chiral symmetry. We investigate topological phase transitions of a model for construction of the two-dimensional second-order topological insulators protected only by chiral symmetry. By the theory of the phase transitions, we propose a second-order topological semimetal and insulators with flat hinge bands in chiral-symmetric three-dimensional systems. The three-dimensional second-order topological phases can be obtained from the stacked two-dimensional second-order topological insulators with chiral symmetry. Moreover, we show that broken chiral symmetry in the three-dimensional second-order topological phase allows a second-order topological insulator with chiral hinge states. We also demonstrate the second-order topological phases by using a lattice model.