We propose a hierarchical stimulus presentation paradigm for a P300-based Hangul (Korean script) input system. A P300-based input system is one of the most promising non-invasive brain-computer interface (BCI) applications based on its direct applicability in many computer programs. While the previous row/column stimulus presentation paradigm has been well-suited to the English input, it may not be optimal for a Hangul input because Hangul has a distinct hierarchical structure. To overcome the limitation of the previous paradigms, we developed a new P300-based Hangul input system by taking the unique hierarchical structure of Hangul into account for creating a hierarchical stimulus presentation paradigm. By using the hierarchical structure, we can effectively reduce the window size of the interface without loss of classification accuracy. A performance comparison shows that the hierarchical paradigm exhibits higher classification accuracy than the row/column paradigm even with a smaller window size. Thus the proposed hierarchical paradigm is more efficient to spell Hangul and will be more useful for BCI-based Hangul input for a text messenger, e-mail program, word processor, and so on.