Provided are a computer program product, system, and method for pre-processing a table in a document for natural language processing. A table in a document is parsed to extract column headers, row headers, and data cells, which are processed to determine an initial 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. A user selection is received of at least one of the column headers, row headers, and data cells for at least one of the main element, conditional element, and the value element in the initial set to produce a modified set of the main element, conditional element, and value element. The modified set is provided to a natural language processing engine to perform natural language processing of the document including the table, using the modified set.