The use of a low-enriched uranium (LEU) fuel target was examined for the feasibility of 99Mo production in a High-flux Advanced Neutron Application Reactor (HANARO). Uncertainty analysis was done with respect to the 99Mo yield ratio, 239Pu yield ratio, annual production rate, and decontamination requirement. Validity of a coupled code system, MCNP/ORIGEN2, was evaluated to estimate reliable isotopic number densities after irradiation and cooling. An equilibrium core model for the MCNP fixed-source problem was found by the reactor design methodology known as WIMS/VENTURE. Optimized target design options were proposed for both the LEU and highly enriched uranium (HEU) targets. Variables related to the target fabrication process and reactor physics condition were considered as uncertainty-inducing parameters. The most important factor affecting the overall uncertainty of the LEU option was the engineering tolerances achievable in the fabrication process of fuel film. The LEU has twice the uncertainty of HEU under current technology, which makes the economics of LEU worse than HEU. It is acceptable, however, in view of the radioactive purity of the alpha emitter because the uncertainty of the impurity level of 239Pu is expected to be relatively small - only 6.5% with a 95% confidence level.