Accurate identification of the locations of endogenous proteins is crucial for understanding their functions in tissues and cells. However, achieving precise cell-type-specific labeling of these proteins has been challenging in vivo. A notable solution to this challenge is the self-complementing split green fluorescent protein (GFP1-10/11) system. In this paper, we present a detailed protocol for labeling endogenous proteins in a cell-type-specific manner using the GFP1-10/11 system in fruit flies. This approach depends on the automatic reconstitution of the GFP1-10 and GFP11 fragments, creating a fluorescence signal. We insert the GFP11 fragment into a specific genomic locus while expressing its counterpart, GFP1-10, through an available Gal4 driver line. The unique aspect of this system is that neither GFP1-10 nor GFP11 alone emits fluorescence, enabling the precise detection of protein localization only in Gal4-positive cells. We illustrate this technique using the adhesion molecule gene teneurin-m (Ten-m) as a model, highlighting the generation and validation of GFP11 protein trap lines via Minos-mediated integration cassette (MiMIC) insertion. Furthermore, we demonstrate the cell-type-specific labeling of Ten-m proteins in the larval brains of fruit flies. This method significantly enhances our ability to image endogenous protein localization patterns in a cell-type-specific manner and is adaptable to various model organisms beyond fruit flies.