Energy‐dispersive X‐ray detectors based on superconducting tunnel junctions (STJs) exhibit at best energy resolution of about 5 eV in full width at half‐maximum for soft X‐rays with energy levels of less than ~1 keV as well as a large sensitive area (>1 mm2) and a high counting rate capability (>500 kcps). We have developed an energy‐dispersive X‐ray spectroscopy analyzer combined with a scanning electron microscope and STJs to realize elemental mapping with high energy‐resolving power. To improve the collection efficiency of the fluorescence X‐rays, a polycapillary collimating X‐ray lens was installed in the analyzer. The overall system efficiency of the analyzer was more than 1 × 10−4 sr in the soft X‐ray range. Its counting rate performance for the N‐Kα line was 9.4 cps/nA, near that of setups comprising an electron probe microanalyzer and wavelength‐dispersive X‐ray spectrometers (WDSs). By improving the X‐ray optics, the counting rate is expected to be increased more than 600‐fold. The energy resolution of the developed analyzer was assessed according to the full width at half‐maximum of the N‐Kα peak, which was measured to be 10 eV, indicating an energy resolution about 7 times better than that of conventional X‐ray spectroscopy analyzers employing silicon drift detectors (SDDs). These results indicate that the improved analyzer employing STJs can realize both the high throughputs of SDDs and the high energy resolution of WDSs. Copyright © 2017 John Wiley & Sons, Ltd.