Functional magnetic resonance imaging (fMRI) of blood oxygenation level dependent (BOLD) signals in the resting state is widely used to study functional connectivity of slowly fluctuating ongoing brain activity (BOLD-FC) in humans, particularly also in patients. While physiological impairments, e.g. aberrant perfusion, are common in neurological and psychiatric disorders, their impact on measured BOLD-FC is widely unknown and ignored. The aim of our simulation study, therefore, was to investigate how alterations in neurovascular coupling influence resting-state BOLD-FC measures. Our results demonstrate crucial impact of neurovascular coupling on BOLD-FC due to changes in CMRO2, CBF, CBV, in both amplitudes and delays.