Anaemia is common in end‐stage heart failure patients supported with continuous flow left ventricular assist device (CF‐LVAD) and is associated with adverse outcomes such as heart failure readmission. This study evaluates the haemodynamic effects of anaemia on cardiac function and cerebral blood flow in heart failure patients supported with CF‐LVAD using computational simulations. A dynamic model simulating cardiac function, systemic, pulmonary and cerebral circulations, cerebral flow autoregulatory mechanisms and gas contents in blood was used to evaluate the effects of anaemia and iron deficiency in heart failure and during CF‐LVAD support. CF‐LVAD therapy was simulated by a model describing HeartMate 3. Anaemia and iron deficiency were simulated by reducing the haemoglobin level from 15 to 9 g/dL and modifying scaling coefficients in the models simulating heart chamber volumes. Reduced haemoglobin levels decreased the arterial O2 content, which increased cerebral blood flow rate by more than 50% in heart failure and during CF‐LVAD assistance. Reduced haemoglobin levels simulating anaemia had minimal effect on the arterial and atrial blood pressures and ventricular volumes. In contrast, iron deficiency increased end‐diastolic left and right ventricular diameters in heart failure from 6.6 cm to 7 cm and 2.9 cm to 3.1 cm and during CF‐LVAD support from 6.1 to 6.4 cm and 3.1 to 3.3 cm. The developed numerical model simulates the effects of anaemia in failing heart and during CF‐LVAD therapy. It is in good agreement with clinical data and can be utilised to assess CF‐LVAD therapy.