Pluto’s icy surface has changed colour and its atmosphere has swelled since its last closest approach to the Sun in 1989. The thin atmosphere is produced by evaporating ices, and so can also change rapidly, and in particular carbon monoxide should be present as an active thermostat. Here we report the discovery of gaseous CO via the 1.3-mm wavelength J=2–1 rotational transition, and find that the line-centre signal is more than twice as bright as a tentative result obtained in 2000 by Bockélee-Morvan et al. Greater surface ice evaporation over the last decade could explain this, or increased pressure could have caused the atmosphere to expand. The gas must be cold, with a narrow line-width consistent with temperatures around 50 K, as predicted for the very high atmosphere, and the line brightness implies that CO molecules extend up to ≈3 Pluto radii above the surface. The upper atmosphere must have changed markedly over only a decade since the prior search, and more alterations could occur by the arrival of the New Horizons mission in 2015.