Biosynthesis and accumulation of jasmonate (JA) can regulate plant defense responses and organ development under insect herbivore stress conditions. One of these responses, the inhibition of root growth, is a common phenomenon. However, the physiological and molecular mechanisms of how JA affects root growth are not completely understood. In this study, the influence of MeJA treatment on auxin and proton flux rates in the root apex region of Col-0, coi1-1, pin2, and aux1-7 mutant lines was examined using a non-invasive micro-test technique. The auxin and H+ flux profiles taken from coi1-1 mutants suggest that the modulation of auxin and H+ flux by JA requires the function of COI1. The auxin and H+ flux in pin2 and aux1 mutants with and without JA treatment suggest that JA can affect polar auxin transport by regulating PIN-mediated auxin efflux and the AUX-mediated influx pathways. Furthermore, the expression levels of PIN1, PIN2, PIN3, PIN7, AUX1, and TIR1 genes were reduced under MeJA treatment, and expression levels of CYP79B2 and CYP79B3 were elevated. Together, these results suggest that JA signaling may modulate the auxin signaling pathways by regulating the expression of key genes.