Phospholipase C-related catalytically inactive proteins (PRIP-1/2) are previously reported to be involved in the membrane trafficking of GABA_A receptor (GABA_AR) and the regulation of intracellular Ca²⁺ stores. GABA_AR-mediated currents can be regulated by the intracellular Ca²⁺. However, in PRIP-1/2 double-knockout (PRIP-DKO) mice, it remains unclear whether the kinetic properties of GABA_ARs are modulated by the altered regulation of intracellular Ca²⁺ stores. Here, we investigated whether GABA_AR currents (I_GABA) evoked by GABA puff in layer 3 (L3) pyramidal cells (PCs) of the barrel cortex are altered in PRIP-DKO mice. The deletion of PRIP-1/2 enhanced the desensitization of I_GABA but induced a hump-like tail current (tail-I) at the GABA puff offset. I_GABA and the hump-like tail-I were suppressed by GABA_AR antagonists. The enhanced desensitization of I_GABA and the hump-like tail-I in PRIP-DKO PCs were mediated by increases in the intracellular Ca²⁺ concentration and were largely abolished by a calcineurin inhibitor and ruthenium red. Calcium imaging revealed that Ca²⁺-induced Ca²⁺ release (CICR) and subsequent store-operated Ca²⁺ entry (SOCE) are more potent in PRIP-DKO PCs than in wild-type PCs. A mathematical model revealed that a slowdown of GABA-unbinding rate and an acceleration of fast desensitization rate by enhancing its GABA concentration dependency are involved in the generation of hump-like tail-Is. These results suggest that in L3 PCs of the barrel cortex in PRIP-DKO mice, the increased calcineurin activity due to the potentiated CICR and SOCE enhances the desensitization of GABA_ARs and slows the GABA-unbinding rate, resulting in their unusual resensitization following removal of GABA.