Chelidonium majus L. is a rich source of isoquinoline alkaloids with confirmed anti-inflammatory, choleretic, spasmolytic, antitumor, and antimicrobial activities. However, their chromatographic analysis is difficult because they may exist both in charged and uncharged forms and may result in the irregular peak shape and the decrease in chromatographic system efficacy. In the present work, the separation of main C. majus alkaloids was optimized using a new-generation XB-C18 endcapped core-shell column dedicated for analysis of alkaline compounds. The influence of organic modifier concentration, addition of salts, and pH of eluents on chromatographic parameters such as retention, resolution, chromatographic plate numbers, and peak asymmetry was investigated. The results were applied to elaborate the optimal chromatographic system for simultaneous quantification of seven alkaloids from the root, herb, and fruit of C. majus.