Precise and controlled drug delivery is crucial in continuous infusion systems used for drug treatment, anesthesia, cancer chemotherapy, and pain management. Elastometric pumps are commonly utilized in continuous infusion systems for their ease of use and cost-effectiveness. However, the infusion accuracy is often compromised due to the fluctuating supply pressure of elastomeric pumps, requiring an additional flow regulator to stabilize the output flow rate. We, here, present a novel approach to passively control a flow rate even under the fluctuating pressure environment based on a channel deformation. The flow rate control is enabled by a flow regulator consisting of an open-end microchannel, a closed-end microchannel, and a flexible membrane in the middle. The pressure within an open-end microchannel decreases in the downstream direction, while the pressure within a closed-end microchannel remains equal to the input pressure, creating the pressure difference between the two channels. The membrane deforms in response to this pressure difference, allowing for adjustment of the output flow rate by decreasing the flow path area with the increase in the input pressure. It is found that this concept successfully works by maintaining a steady output flow rate over a target pressure range of 40–50 kPa. Fluid–structure interaction numerical simulations and theoretical analysis are used to explain the flow rate control mechanism of the device. The results show that the present approach offers a promising solution for achieving stable drug delivery in continuous drug infusion systems, addressing the limitations of conventional elastomeric pumps.