The increasing demand for robotic applications has emphasized the need for advanced control strategies, particularly for flexible manipulators with lightweight links. These manipulators offer advantages such as reduced energy consumption, increased payload capacity, and precise high-speed operation but face challenges due to oscillations and delays caused by their flexibility. This study evaluates the performance of Fuzzy Logic Control (FLC) and Linear Quadratic Regulator (LQR) techniques for a Quanser two-link flexible manipulator, using quantitative metrics to compare their effectiveness. The LQR controller was implemented using state-space modeling, with weighting matrices Q and R tuned to achieve minimal overshoot and fast settling times. The FLC system employed five triangular membership functions for inputs and outputs, covering normalized ranges of [-1, 1] for angular errors and [-2.75, 2.75] for error rates, with a heuristic rule base designed to optimize performance. Simulations were conducted under step input conditions at target angles of 30° and 60°, with performance evaluated using vibration amplitude, settling time, steady-state error, and overshoot. Quantitatively, the LQR controller reduced vibration amplitudes to 5 radians for a 30° input and achieved settling times of approximately 2 seconds. For the same conditions, the FLC system reduced vibrations further to 4 radians, though with slightly longer settling times of around 2.3 seconds. At a 60° input, LQR vibrations peaked at over 10 radians, while FLC maintained peak vibrations at approximately 4 radians. These results highlight the FLC’s superior vibration suppression, particularly at higher input angles, albeit with marginally slower response times. However, the study was limited to idealized simulation conditions and requires further experimental validation. This research underscores the trade-offs between LQR’s precision and FLC’s adaptability, emphasizing the importance of parameter tuning and system modeling in achieving optimal performance for flexible manipulators.