All-sky surveys are crucial to discover transient objects. In reality, however, it is impossible to achieve high sensitivity, high cadence, wide sky coverage, and broad wavelength range at the same time. This is where observations with small telescopes can come in significant, as small telescopes often can make high cadence monitoring and flexible operations, playing a complementary role to large observatories. We plan to launch a new 6U-size CubeSat X-ray observatory, NinjaSat, in 2022 to conduct a flexible X-ray observation program. The satellite is equipped with two identical non-imaging Gas Multiplier Counters (GMCs) sensitive to X-rays in the 2–50 keV band with a total effective area of 36 cm2 at 6 keV. Coupled with X-ray collimators of a 2.1° field-of-view, NinjaSat is suitable for flexible multi-wavelength coordinated observations of bright (⪆10 mCrab) X-ray sources with particular emphasis on their time variability. An example of our targets is one of the brightest celestial X-ray objects, Scorpius X-1, which hosts a fast-spinning neutron star and is a candidate source for coherent gravitational waves. The quasi-periodic oscillation (QPO) of neutron-star systems is considered to carry important information on the neutron star’s rotational frequency, which is useful for sensitive gravitational-wave searches. Scorpius X-1, being one of the brightest, provides the best opportunity to study the QPO. Combining with coordinated simultaneous monitoring observations with recently-developed fast optical photometry, the mechanism of the mass accretion of the disk can also be studied. We plan to use NinjaSat also for space science education, particularly X-ray astronomy, for students and the general public.