The energy storage deployment becomes necessary as more renewable energy sources are being installed to achieve sustainable energy access in off-grid areas. Battery prices, however, still hinder massive deployment. One of the energy storage technologies being developed for microgrid applications are flywheels, which stores energy through rotational kinetic energy and are typically suited for high power applications. With the advent of long-discharge flywheels, such as those being marketed by Amber Kinetics® and Beacon Power®, they can be used in microgrids, which are dominated by batteries. This study provides a techno-economic comparison with sensitivity analysis between long-discharge flywheel and utility-scale lithium-ion battery for microgrid applications. The results show lowest levelized cost of electricity (LCOE) for flywheel-based hybrid energy system with 0.345 USD/kWh and renewable share of 62.4 % among tested configurations. The competitiveness of long-discharge flywheel over lithium-ion battery in the microgrid market depends on the diesel prices, expected reduction in lithium-ion battery prices, and improvements in lithium-ion battery lifespan.