G protein-coupled receptors (GPCRs) form a superfamily of approximately 800–1000 receptors, including cell surface receptors that are internalized with activation and recycled to the plasma membrane. Over 50% of GPCR mRNAs and the open reading frames are comprised of multiple exons, and splice variant isoforms have been identified. These isoforms differ in pharmacological ligand bias, cellular location, and functional outputs. Alternative splicing of mRNAs is a major mechanism in nature to create diversity from single genes and expansion of protein arrays that are tissue specific. Alternative splicing is a dominant phenomenon in tumor transformation, expansion, and survival that generates new proteins with diverse functions and provides tumors with the machinery to survive in hostile microenvironments. High-grade tumors have unique tissue hierarchies and include relatively undifferentiated, proliferating malignant cells, and quiescent cancer stem cells (CSCs), which are largely resistant to conventional therapies that normally target dividing cells. CSCs are responsible for minimal residual disease. New strategies aimed at treating quiescent CSCs that express splice variants of GPCRs are presented and discussed. Antibodies and antibody-like scaffolds including diabodies, nanobodies, i-bodies, and DARPins are discussed as possible targeting moieties for GPCRs and splice variants, which may be pharmacologically inactive. The clinical development of the antibody-like scaffolds provides the opportunity for tissue penetration and pharmacokinetic stability with the targeting of specific cell types in diseases. Case studies of these targeting entities for GPCRs are presented that are currently under preclinical development or in clinical trials for the treatment of cancers.