The exchange of energy and momentum between the Earth's upper atmosphere and ionosphere, and its space environment (magnetosphere) is regulated by electric currents (called Birkeland currents) flowing along magnetic field lines that connect these two regions of space1. The associated electric currents flow towards and away from each pole primarily in two concentric conical sheets2. It has been expected that powerful sheets of magnetic-field-aligned electric currents would be found in association with the bright Jovian auroras3. The Juno spacecraft is well positioned to explore Jupiter's polar magnetosphere and sample Birkeland or field-aligned currents and particle distributions. Since July 2016, Juno has maintained a near-polar orbit, passing over both polar regions every 53 days. From this vantage point, Juno's complement of science instruments gathers in situ observations of magnetospheric particles and fields while its remote-sensing infrared and ultraviolet spectrographs and imagers map auroral emissions4. Here we present an extensive analysis of magnetic field perturbations measured during Juno's transits of Jupiter's polar regions, and thereby demonstrate Birkeland currents associated with Jupiter's auroral emissions. We characterize the magnitude and spatial extent of the currents and we find that they are weaker than anticipated and filamentary in nature. A significant asymmetry is observed between the field perturbations and the current associated with the northern and the southern auroras.