Updated publication reference for PubMed record(s): 29930108. Obtaining a systems view of G protein-coupled receptor (GPCR) signaling in its native environment is the key in development of GPCR therapeutics with fewer side effects. Using the kappa opioid receptor (KOR) as model GPCR, we employed high-throughput phosphoproteomics to investigate downstream signaling induced by structurally diverse agonists in five mouse brain-regions. Through quantification of 50,000 different phosphosites, this approach yielded a systems view of KOR in vivo signaling, revealing novel mechanisms of drug action. Pathway-selective agonists elicited differential dynamic phosphorylation of synaptic proteins, linking GPCR signaling to modulation of brain functions. We also discovered enrichment of mTOR pathway in agonists associated with aversion, a side effect. Consequently, mTOR inhibition during KOR activation abolished aversion, while preserving therapeutic analgesic and anticonvulsant effects. Our results establish high-throughput phosphoproteomics as a general strategy to investigate GPCR in vivo signaling, enabling prediction and modulation of behavioral outcomes.