Toll-like receptors (TLRs) are type I transmembrane proteins that are key regulators of both innate and adaptive immune responses. To protect the host from viral and bacterial threats, TLRs trigger a pro-inflammatory immune response by detecting pathogen and danger associated molecular patterns. Considerable evidence has accumulated to show that the dysregulation of TLR signaling contributes to the development and progression of numerous diseases. Therefore, TLRs are emerging as important drug discovery targets. Currently, there is great interest in the development of TLR small molecule modulators for interrogating TLR signaling and treating diseases caused by TLR signaling malfunctions. In this tutorial review, we will outline methods for the discovery of TLR small molecule modulators and the up-to-date progress in this field. Small molecules targeting TLRs not only provide an opportunity to identify promising drug candidates, but also unveil knowledge regarding TLR signaling pathways.