In the paper [KW2] we introduced a new type of Selberg zeta function for establishing a certain identity among the non-trivial zeroes of the Selberg zeta function and of the Riemann zeta function. We shall call this zeta function a higher Selberg zeta function. The purpose of this paper is to study the analytic properties of the higher Selberg zeta function z(Gamma)(s), especially to obtain the functional equation. We also describe the gamma factor of z(Gamma)(s) in terms of the triple sine function explicitly and, further, determine the complete higher Selberg zeta function with having a discussion of a certain generalized zeta regularization.