We present a search for continuous gravitational-wave emission due to r-modes in the pulsar PSR J0537–6910 using data from the LIGO–Virgo Collaboration observing run O3. PSR J0537–6910 is a young energetic X-ray pulsar and is the most frequent glitcher known. The inter-glitch braking index of the pulsar suggests that gravitational-wave emission due to r-mode oscillations may play an important role in the spin evolution of this pulsar. Theoretical models confirm this possibility and predict emission at a level that can be probed by ground-based detectors. In order to explore this scenario, we search for r-mode emission in the epochs between glitches by using a contemporaneous timing ephemeris obtained from NICER data. We do not detect any signals in the theoretically expected band of 86–97 Hz, and report upper limits on the amplitude of the gravitational waves. Our results improve on previous amplitude upper limits from r-modes in J0537-6910 by a factor of up to 3 and place stringent constraints on theoretical models for r-mode-driven spin-down in PSR J0537–6910, especially for higher frequencies at which our results reach below the spin-down limit defined by energy conservation.