Hydrocarbon species, and in particular CH4, play a key role in the stratosphere-thermosphere boundary of Jupiter, which occurs around the μ-bar pressure level. Previous analyses of solar occultation, He and Ly-α airglow, and ISO/SWS measurements of the radiance around 3.3 μm have inferred significantly different methane concentrations. Here we aim to accurately model the CH4 radiance at 3.3 μm measured by ISO/SWS by using a comprehensive non-local thermodynamic equilibrium model and the most recent collisional rates measured in the laboratory for CH4 to shed new light onto the methane concentration in the upper atmosphere of Jupiter. These emission bands have been shown to present a peak contribution precisely at the μ-bar level, hence directly probing the region of interest. We find that a high CH4 concentration is necessary to explain the data, in contrast with the most recent analyses, and that the observations favour the lower limit of the latest laboratory measurements of the CH4 collisional relaxation rates. Our results provide precise constraints on the composition and dynamics of the lower atmosphere of Jupiter.