The magnetic, thermodynamic and electrical/thermal transport properties of the caged-structure quasi-skutterudite Gd$_3$Ir$_4$Sn$_{13}$ are re-investigated. The magnetization $M(T)$, specific heat $C_p(T)$ and the resistivity $rho(T)$ reveal a double-phase transition -- at $T_{N1}sim$ 10~K and at $T_{N2}sim$ 8.8~K -- which was not observed in the previous report on this compound. The antiferromagnetic transition is also visible in the thermal transport data, thereby suggesting a close connection between the electronic and lattice degrees of freedom in this Sn-based quasi-skutterudite. The temperature dependence of $rho(T)$ is analyzed in terms of a power-law for resistivity pertinent to Fermi liquid picture. Giant, positive magnetoresistance (MR) $approx$ 80$%$ is observed in Gd$_3$Ir$_4$Sn$_{13}$ at 2~K with the application of 9~T. The giant MR and the double magnetic transition can be attributed to the quasi-cages and layered antiferromagnetic structure of Gd$_3$Ir$_4$Sn$_{13}$ vulnerable to structural distortions and/or dipolar or spin-reorientation effects. The giant value of MR observed in this class of 3:4:13 type alloys, especially in a Gd-compound, is the highlight of this work.