Magnetic tweezers, a micromanipulation method that can apply and measure physical forces of a broad range of amplitudes without direct contact, are practical for studying the mechanical properties of the cell interior. However, owing to the hysteresis of magnetic materials, it is generally difficult to control the force amplitude of magnetic tweezers in real time, hindering their use in probing intracellular mechanics on short timescales. Herein, we present a simple and versatile method that can precisely control magnetic forces with a response time of submilliseconds. This method adopts a reconfigurable hardware platform to realize fast digital proportional–integral–derivative (PID) feedback control of the electromagnet. The digital PID system allows us to readily implement different core materials, including hard magnetic materials, for precise measurements. Taking advantage of the programmability of the system, we propose a magnetization protocol to reduce the Joule heat generated by the coil current. We demonstrate that the developed high-speed magnetic tweezers enable characterization of the cytoplasmic rheology of living cells over four orders of magnitude in timescale from a single creep measurement. This method provides a powerful tool for investigating cellular phenomena from the perspective of soft matter physics.