The present invention relates to an oral pharmaceutical composition containing pemetrexed as a water-soluble anticancer drug and a method of manufacturing the same, and more particularly to an oral pharmaceutical composition, in which an ion-binding complex of pemetrexed and a bile acid derivative as an oral absorption enhancer is formed, mixed with a pharmaceutical additive, and then provided in the form of a capsule or a tablet through pressing or included in the internal water phase of a w/o/w (water-in-oil-in-water) multiple nanoemulsion, thus increasing the oral bioavailability of pemetrexed as the water-soluble anticancer drug, whereby pemetrexed, which is currently administered only in the form of an injection formulation, can be manufactured into a formulation capable of being orally administered, ultimately alleviating inconvenience and problems with use of injection formulations, improving patient compliance and contributing to a reduction in medical expenses.