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We introduce an algebraically active disturbance rejection-based control solution for the trajectory tracking problem of an uncertain second-order flat system with unknown external disturbances. To this end, we first algebraically identify the system’s unknown dynamics and the external disturbances with a linear set of time-varying integral expressions for the output and the control signal. We use the identified dynamics on an online feedback cancellation scheme to linearize the second-order system and cancel the uncertainties. With a proportional-integral controller we stabilize the linearized system without the need to estimate the velocity and have feedback from it. We carry out the stability analysis using linear systems theory. Finally, we evaluate the effectiveness of the proposed controller in a partially known 2-DOF manipulator.