PathwayConnector is a web-tool that facilitates the construction of complementary pathway-to-pathway networks and subnetworks of them, based on a reference pathway network derived from the rich information available either in KEGG or Reactome database for pathway mapping. Specifically, for a given set of pathways, PathwayConnector (i) finds all the direct connections between them, (ii) adds a minimum set of complementary pathways required to achieve connectivity between the pathways, leading to informative fully connected networks and (ii) provides a series of clustering methods for the further grouping of pathways in to sub-clusters. The proposed web-tool is a simple yet informative tool towards identifying connected groups of pathways that are significantly related to specific diseases.