Provided are a computer program product, system, and method for pre-processing a table in a document for natural language processing (NLP). A graphical user interface (GUI) provides a representation of table items in a table in a document including a set of a main element comprising an entity whose value is to be extracted, a conditional element that refines the entity, and a value element comprising a value for the entity. Graphical controls are rendered in the GUI to enable a user to select an element from the table to be the main element, conditional element, and value element. The set of the main element, conditional element, and value element are updated with the user selected element to form a modified set. The modified set of the main element, conditional element, and the value element are provided to an NLP engine to perform natural language processing.