Selective pharmacological tool compounds are invaluable for understanding the functions of the various ionotropic glutamate receptor subtypes. For the kainate receptors these compounds are few. Here we have synthesized 9 novel quinoxaline-2,3-diones with substitutions in the 7-position to investigate the structure-activity relationship at kainate and AMPA receptors. Compound 11 exhibited the highest binding affinity across GluK1-3 while having a 73-fold selectivity towards kainate vs. AMPA receptors. 11 potently inhibited glutamate evoked currents at homomeric GluK1 and GluK3 receptors in HEK293 cells with Kb values of 65 and 39 nM, respectively. The binding mode of 11 in the ligand binding domain of GluK1 was investigated by X-ray crystallography, revealing that 11 stabilizes the receptor in an open conformation, consistent with its demonstrated antagonism. Furthermore, 11 was tested for analgesic effects in the mouse tail flick test where it significantly increased tail flick latency at doses where NBQX was ineffective.