Iron plays important physiological and pathological roles in the human body. However, microscopic analysis including redox status by a conventional electron spin resonance (ESR) spectrometer is difficult due to limited spatial resolution and sensitivity. Here we demonstrate magnetometry of cultured neurons on a polymeric film using a superconducting flux qubit that works as a sensitive magnetometer in a microscale area towards realizing ESR spectroscopy. By changing temperature (12.5–200 mK) and a magnetic field (2.5–12.5 mT), we observe a clear magnetization signal from the neurons that is well above the control magnetometry of the polymeric film itself. From ESR spectrum measured at 10 K, the magnetization signal is identified to originate from electron spins of iron ions in neurons. This technique to detect a bio-spin system can be extended to achieve ESR spectroscopy at the single-cell level, which will give the spectroscopic fingerprint of cells.