The permeation of 1-ethyl-3-methylimidazolium ([EMIM]), 1-butyl-3-methylimidazolium ([BMIM]), and 1-butylimidazole through the bilayer membranes of nanoemulsion-like polymersomes was investigated by nuclear magnetic resonance spectroscopy (NMR) techniques. 1,2-Polybutadiene-b-poly(ethylene oxide) (PB-PEO) polymersomes in the ionic liquid (IL) 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([EMIM][TFSI]) were prepared by a cosolvent method and then migrated to the aqueous phase, which is not miscible with the IL, at room temperature. In this way stable, nanoscopic domains of the IL (average diameter ca. 200 nm) were dispersed in water. Two similarly sized molecules, charged [EMIM] and neutral 1-butylimidazole, were employed as tracer molecules, and proton NMR (1H NMR) and pulsed-field-gradient NMR (PFG-NMR) experiments were conducted. Furthermore, transient 1H NMR was used with [BMIM] to estimate how rapidly the charged molecules can go through the hydrophobic membrane into the polymersome interior. The molecules in the nanoemulsion solution showed two distinct sets of peaks due to the magnetic susceptibility difference across the membrane. This difference in 1H NMR gave direct evidence of permeation of the molecules and the relative populations within the polymersomes versus in the aqueous exterior. The escape and entry rates were evaluated by fitting the PEG-NMR echo decay curves with a two-site exchange model. The molecules could permeate through the hydrophobic PB membranes on a time scale of seconds, but the entry and escape rates for the charged molecule ([EMIM]) were approximately 10 times slower than the neutral molecule (1-butylimidazole). These results confirm that this system has the potential to serve as a nanoreactor, facilitating reactions with various kinds of molecules including both charged and neutral molecules. It combines the facile transport and mixing of a majority aqueous phase with the multiple advantages of IL as a reaction medium. The ability to shuttle the polymersomes reversibly between aqueous and ionic liquid phases offers a convenient route to product separation and catalyst recovery.