The aberrant accumulation of cytotoxic protein aggregates is a hallmark of various neurodegenerative and non‐neurodegenerative ailments, necessitating the development of sensitive and selective tools for their detection. Herein, we report a series of morpholine‐anchored fluorescent probes, denoted as SC‐nmor (n = 2, 4, 6), designed for facile visualization of protein aggregates. These probes display notable changes in their photophysical properties upon binding with protein aggregates, owing to their high sensitivity to the fibrillar microenvironment. Specifically, the SC‐4mor probe demonstrates strong selectivity for aggregated insulin proteins over native insulin, accompanied by a significant enhancement in fluorescence lifetime. Live‐cell imaging reveals an exclusive localization at the lysosomal compartment. This feature enables the visualization of lysosomal accumulated protein fibrils induced with pepstatin A. Additionally, in vivo assessments on genetically mutated and dietary‐modified Drosophila melanogaster, representing neurodegenerative and non‐neurodegenerative disease models, demonstrate staining of protein aggregates. The enhanced emission from the eye lobes of Aβ‐mutated and HSD brain samples, suggesting that SC‐4mor can exhibit adequate retention in the brain with minimal biological toxicity. SC‐4mor also shows its capability to cross the blood–brain barrier in mice model. Consequently, SC‐4mor emerges as a promising marker for detecting and monitoring neurotoxic protein fibrillation in live cells and animal models, offering potential insights into the pathogenesis and progression of protein aggregation.