Different energy storage technologies can be potentially integrated into microgrids to support variable renewable energy generators. Long-duration flywheel energy storage is considered a new contender in the energy storage market. This energy storage technology has been previously evaluated in a techno-economic study, but it did not consider uncertainties in the model input data. In this work, stochastic techno-economic comparison is performed using microgrid modeling and Monte-Carlo methods to compare long-duration flywheels, lithium-ion batteries, and lead-acid batteries for isolated microgrid and industrial facility. Results generally show a relatively high probability for long-duration flywheels to yield a lower leveized cost of storage (LCOS) and levelized cost of electricity (LCOE) compared to lithium-ion batteries in 2020. Higher probability can be attained when the overnight component cost of long-duration flywheels is reduced or when overnight diesel prices are high. However, the chances of long-duration flywheels yielding lower LCOS and LCOE rapidly decreases as time progresses. Long-duration flywheel manufacturers and promoters must find ways to accelerate price reduction by 2.5× from baseline to secure a better chance of yielding a lower LCOS in 2050.