Abstract The exceptionally favorable close approach of Jupiter-family comet 46P/Wirtanen in 2018 December enabled characterization of its primary volatile composition with exceptionally high spatial resolution and sensitivities using the iSHELL spectrograph at the NASA Infrared Telescope Facility on Maunakea, HI. We sampled emissions from H2O, HCN, C2H2, NH3, C2H6, and CH3OH on UT 2018 December 21 using two instrumental settings that spanned the 2.9–3.6 μm spectral region. We also obtained a sensitive 3σ upper limit for H2CO and for the rarely studied molecule HC3N. We report rotational temperatures, production rates, and mixing ratios (relative to H2O as well as to C2H6). We place our results in context by comparing them with other comets observed at near-IR wavelengths. We also compare our results with those obtained using the NIRSPEC-2 spectrograph on Keck II on UT December 17 and 18 and with results obtained from iSHELL on other dates during the same apparition. Within 1–2σ uncertainty, production rates obtained for all molecules in this work were consistent with those obtained using NIRSPEC-2 except H2O, indicating low-level variability on a timescale of days. Mixing ratios with respect to H2O in 46P/Wirtanen were consistent with corresponding values from NIRSPEC-2 within the uncertainty with the exception of CH3OH, which yielded a higher ratio on December 21. Our measurements afforded a high temporal resolution that spanned ∼2/3 of the rotational period of 46P/Wirtanen, enabling us to test short-term variability in the production rates of H2O and HCN due to rotational effects. Both H2O and HCN production rates showed similar temporal variability, resulting in nearly constant HCN/H2O.