Neurodegenerative diseases, including Alzheimer’s disease (AD), represent one of the main global health challenges. Cannabis sativa synthesizes spermidine-type alkaloids, whose potential biological activities have been little studied. This study aimed to isolate bioactive alkaloids from an alkaloid-enriched extract (AEE) of C. sativa roots throughout a bioguided approach using conventional chromatographic techniques based on AChE and BuChE inhibitory activities. A qualitative and semiquantitative analysis by UPLC-ESI-MS/MS as well as molecular modeling simulations were performed. In addition, predictive in silico analyses were conducted to assess toxicity properties. The alkaloids cannabisativine (CS) and anhydrocannabisativine (ACS) were isolated, and showed highly selective BuChE inhibitory activity. The molecular modeling study revealed a conserved interaction profile across both alkaloids, indicating the amino acids TRP82, GLU197, TYR440, and HIS438 as the major contributors involved in the complex formation. Finally, CS and ACS exhibited low in silico predictive toxicity values. In conclusion, CS and ACS alkaloids emerge as new selective BuChE inhibitors with therapeutic potential that deserves the attention from the field of pharmacology in neurodegenerative disease research. Additionally, this approach promotes innovation and environmental sustainability through the use of C. sativa roots.