A simple and selective method for the determination of caffeine (CAF) and theophylline (THEO) has been developed for a glassy carbon electrode (GCE) modified with a composite including carbon dots (CDs) and chitosan (CS). To our knowledge, there are no previous studies that analyze a CDs-modified GCE for the presence of CAF and THEO. The electrochemical behavior of a GCE modified with a CDs-CS composite was studied in acidic medium by cyclic voltammetry (CV) and differential pulse voltammetry (DPV). Considering the sensor analytical parameters, the same linear concentrations range was found for CAF and THEO ranging from 1 × 10−5 to 5 × 10−3 mol L−1 with the same detection limit (LOD) of 1 × 10−6 mol L−1. The reproducibility and repeatability data were satisfactory in terms of RSD%. Moreover, the storage stability was evaluated, evidencing good results whatever the experimental conditions used. The developed sensor was applied for the simultaneous determination of CAF and THEO in tea and drug, and results were compared with those obtained with HPLC-ESI-MS in SIR mode as an independent method optimized on purpose. The electrochemical sensor presents the undoubled advantages in terms of cheapness, portability, and ease of use, since it does not require skilled personnel.