Abstract NinjaSat is an X-ray CubeSat designed for agile, long-term continuous observations of bright X-ray sources, with the size of 6U ($112.7\times 237.1\times 340.5$ mm3) and a mass of 8 kg. NinjaSat is capable of pointing at X-ray sources with an accuracy of less than $0.^{\!\!\!\circ }1$ ($2\sigma$ confidence level) with three-axis attitude control. The satellite bus is a commercially available NanoAvionics M6P, equipped with two non-imaging gas X-ray detectors covering an energy range of 2–50 keV. A total effective area of 32 cm2 at 6 keV is capable of observing X-ray sources with a flux of approximately $10^{-10}$ erg cm−2 s−1. The arrival time of each photon can be tagged with a time resolution of $61\, \mu$s. The two radiation belt monitors continuously measure the fluxes of protons above 5 MeV and electrons above 200 keV trapped in the geomagnetic field, alerting the X-ray detectors when the flux exceeds a threshold. The NinjaSat project started in 2020. Fabrication of the scientific payloads was completed in 2022 August, and satellite integration and tests were completed in 2023 July. NinjaSat was launched into a Sun-synchronous polar orbit at an altitude of about 530 km on 2023 November 11 by the SpaceX Transporter-9 mission. After about three months of satellite commissioning and payload verification, we observed the Crab Nebula on 2024 February 9 and successfully detected the 33.8262 ms pulsation from the neutron star. With this observation, NinjaSat met the minimum success criterion and stepped forward to scientific observations as initially planned. By the end of 2024 November, we successfully observed 21 X-ray sources using NinjaSat. This achievement demonstrates that, with careful target selection, we can conduct scientific observations effectively using CubeSats, contributing to time-domain astronomy.