Alternative splicing of latrophilin-3 (LPHN3) regulates synapse formation in the hippocampus. LPHN3 is a postsynaptic adhesion G-protein-coupled receptor (GPCR) that binds to presynaptic teneurin and FLRT adhesion molecules. The study shows that LPHN3 undergoes extensive alternative splicing, resulting in different G-protein coupling modes. The predominant splice variant in the brain couples to Gαs and is essential for synapse formation. This variant also recruits phase-separated postsynaptic protein scaffolds, which are clustered by binding of presynaptic teneurin and FLRT ligands to LPHN3. Neuronal activity promotes alternative splicing of the Gαs-coupled variant of LPHN3, enhancing its expression. The study demonstrates that the Gαs-coupled variant of LPHN3 is crucial for synapse formation through two convergent pathways: Gαs signaling and clustered phase separation of postsynaptic protein scaffolds. The C-terminal sequence of LPHN3, encoded by E31, is essential for recruiting postsynaptic scaffold proteins. The PBM of E31 interacts with SHANK scaffold proteins, and its deletion disrupts synapse formation. The study also shows that the Gαs-coupled variant of LPHN3 is required for synaptic connectivity, and its deletion impairs synaptic connectivity as severely as the overall deletion of LPHN3. The findings highlight the role of alternative splicing in regulating synapse formation by enabling precise control through neuronal activity.Alternative splicing of latrophilin-3 (LPHN3) regulates synapse formation in the hippocampus. LPHN3 is a postsynaptic adhesion G-protein-coupled receptor (GPCR) that binds to presynaptic teneurin and FLRT adhesion molecules. The study shows that LPHN3 undergoes extensive alternative splicing, resulting in different G-protein coupling modes. The predominant splice variant in the brain couples to Gαs and is essential for synapse formation. This variant also recruits phase-separated postsynaptic protein scaffolds, which are clustered by binding of presynaptic teneurin and FLRT ligands to LPHN3. Neuronal activity promotes alternative splicing of the Gαs-coupled variant of LPHN3, enhancing its expression. The study demonstrates that the Gαs-coupled variant of LPHN3 is crucial for synapse formation through two convergent pathways: Gαs signaling and clustered phase separation of postsynaptic protein scaffolds. The C-terminal sequence of LPHN3, encoded by E31, is essential for recruiting postsynaptic scaffold proteins. The PBM of E31 interacts with SHANK scaffold proteins, and its deletion disrupts synapse formation. The study also shows that the Gαs-coupled variant of LPHN3 is required for synaptic connectivity, and its deletion impairs synaptic connectivity as severely as the overall deletion of LPHN3. The findings highlight the role of alternative splicing in regulating synapse formation by enabling precise control through neuronal activity.