-Flexible manipulators have several benefits over the rigid manipulators such as light weight with higher payload, better maneuverability, higher operational speed, lower energy consumption. Along these advantages, however, the flexible manipulators cause vibrations and trajectory tracking control problems. In this study, a cascade interval type-2 fuzzy logic controller (IT2FL-C) was proposed for real time trajectory and vibration control of a flexible joint manipulator. The proposed controller was implemented in the system using dSpace DS1103 real-time control board. The cascade control structure includes three separate IT2FL-C. The IT2FL-Cs were designed on the IT2FL-C toolbox, which we developed, with interval triangular membership functions (MFs), Mamdani's fuzzy inference method and Karnik-Mendel (KM) type reduction (TR) algorithm. Several experiments conducted for observation of the proposed IT2FL-C's performance. The step and sinusoidal trajectories were applied to the system changing link length with/without external payload. Additionally, performance of the proposed controllers was compared to conventional type-1 fuzzy logic controller (T1FL-C).