"Regulators of G protein signaling" (RGS proteins) have profound effects on ion channels regulated by G protein-coupled receptor (GPCR) signaling, including the G protein-gated inwardly rectifying K+ (GIRK) channels that inhibit excitability of neuronal, endocrine, and cardiac cells. Here we describe the effects of an alternatively spliced "short" RGS3 isoform (RGS3s) in comparison to RGS4, on the temporal and steady-state gating properties of neuronal GIRK channels (Kir3.1/Kir3.2a) activated by either serotonin 1A (5-HT(1A)) receptors or muscarinic m2 receptors expressed in Chinese hamster ovary (CHO-K1) cells. RGS3s is abundantly expressed in brain and contains a unique short N-terminus via alternative splicing that distinguishes it from other RGS3 isoforms as well as other members of the B/R4 RGS gene subfamily. Our results indicate that RGS3s and RGS4 similarly affect the temporal and steady-state gating properties of 5-HT(1A) receptor-coupled Kir3.1/Kir3.2a channels, but differentially modulate muscarinic m2 receptor-coupled channels. RGS3s caused a significant approximately 45% reduction in the maximal acetylcholine (ACh)-evoked GIRK current amplitude and a marked shift in the steady-state ACh dose-response relation indicative of a reduction in functionally coupled m2 receptor-GIRK channel complexes. Yet RGS3s still accelerated the m2 receptor-dependent GIRK activation, deactivation, and acute desensitization time course consistent with the RGS-enhanced GAP activity that was also observed with RGS4. Several mechanisms that may contribute to the receptor-dependent effects of RGS3s are discussed with particular attention to the role of the distinct N-terminal domain. Our findings highlight the potential impact of selective RGS-GPCR interactions on neuronal GIRK channel function that may affect the properties of inhibitory postsynaptic potentials activated by different GPCR-GIRK channel complexes.