In our previous work (Y. Hashimoto, Selberg’s zeta function for the modular group in the critical strip, Math. Nachr. 294 (2021) 1899–1904, https://doi.org/10.1002/mana.202000268 ), we proposed an upper bound of the logarithmic derivative of Selberg’s zeta function for the modular group in the critical strip. This paper studies the growth of its square integral for the modular group, co-compact arithmetic groups derived from indefinite quaternion algebras and their subgroups.