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In this study, we present a sensorless, robust, and physiological tracking control method to drive the operational speed of implantable rotary blood pumps (IRBPs) for patients with heart failure (HF). The method used sensorless measurements of the pump flow to track the desired reference flow (<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mrow><msub><mi>Q</mi><mi>r</mi></msub></mrow></semantics></math></inline-formula>). A dynamical estimator model was used to estimate the average pump flow (<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mrow><msub><mover><mi>Q</mi><mo stretchy="false">^</mo></mover><mrow><mi>e</mi><mi>s</mi><mi>t</mi></mrow></msub></mrow></semantics></math></inline-formula>) based on pulse-width modulation (PWM) signals. A proportional-integral (PI) controller integrated with a fuzzy logic control (FLC) system was developed to automatically adapt the pump flow. The <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mrow><msub><mi>Q</mi><mi>r</mi></msub></mrow></semantics></math></inline-formula> was modeled as a constant and trigonometric function using an elastance function (<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mrow><mi>E</mi><mo stretchy="false">(</mo><mi>t</mi></mrow></semantics></math></inline-formula>)) to achieve a variation in the metabolic demand. The proposed method was evaluated in silico using a lumped parameter model of the cardiovascular system (CVS) under rest and exercise scenarios. The findings demonstrated that the proposed control system efficiently updated the pump speed of the IRBP to avoid suction or overperfusion. In all scenarios, the numerical results for the left atrium pressure (<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mrow><msub><mi>P</mi><mrow><mi>l</mi><mi>a</mi></mrow></msub></mrow></semantics></math></inline-formula>), aortic pressure (<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mrow><msub><mi>P</mi><mrow><mi>a</mi><mi>o</mi></mrow></msub></mrow></semantics></math></inline-formula>), and left ventricle pressure (<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mrow><msub><mi>P</mi><mrow><mi>l</mi><mi>v</mi></mrow></msub></mrow></semantics></math></inline-formula>) were clinically accepted. The <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mrow><msub><mover><mi>Q</mi><mo stretchy="false">^</mo></mover><mrow><mi>e</mi><mi>s</mi><mi>t</mi></mrow></msub></mrow></semantics></math></inline-formula> accurately tracked the <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mrow><msub><mi>Q</mi><mi>r</mi></msub></mrow></semantics></math></inline-formula> within an error of 0.25 L/min.