Induced pluripotent stem cells (iPSCs) are a powerful tool for neural regeneration and the treatment of neurodegenerative diseases. A major challenge in this field is optimizing the differentiation of iPSCs into functional neurons. C-Phycocyanin (C-PC), a protein derived from blue-green algae, has garnered attention for its antioxidant properties and regulatory effects on cellular signaling pathways, including the Notch pathway. This review explores the impact of CPC on key molecules in the Notch pathway, such as NOTCH1, HES1, and JAGGED1, which play critical roles in regulating neural differentiation. The Notch pathway contributes to maintaining the pluripotency of stem cells by modulating the expression of genes like HES1, and C-PC may facilitate neuronal differentiation through its effects on this pathway. Furthermore, recent evidence suggests that specific long non-coding RNAs (lncRNAs), including MALAT1, and TUG1, interact with the Notch pathway and influence iPSC differentiation into neurons. This review highlights the potential role of C-PC in regulating these lncRNAs and their interplay with Notch pathway components. Understanding the mechanisms through which C-PC influences neuronal differentiation offers significant potential for advancing regenerative medicine. By targeting the Notch pathway and associated molecular networks, C-PC could serve as a novel therapeutic agent to enhance the efficiency and precision of iPSC-based neuronal differentiation. This opens exciting possibilities for treating neurodegenerative disorders such as Parkinson’s and Alzheimer’s disease, where neuronal loss is a hallmark. Future research should investigate how C-PC can be applied in stem cell research and its potential to revolutionize personalized therapies by influencing the Notch pathway and lncRNAs.