We present high-speed optical photometry of the anomalous X-ray pulsar 1E1048.1-5937 obtained with ULTRACAM on the 8.2-m Very Large Telescope in 2007 June. We detect 1E1048.1-5937 at a magnitude of i' = 25.3 +/- 0.2, consistent with the values found by Wang et al. and hence confirming their conclusion that the source was approximately 1mag brighter than in 2003-06 due to an on-going X-ray flare that started in 2007 March. The increased source brightness enabled us to detect optical pulsations with an identical period (6.458s) to the X-ray pulsations. The root-mean-square (rms) pulsed fraction in our data is 21 +/- 7 per cent, approximately the same as the 2-10keV X-ray rms pulsed fraction. The optical and X-ray pulse profiles show similar morphologies and appear to be approximately in phase with each other, the latter lagging the former by only 0.06 +/- 0.02 cycles. The optical pulsations in 1E1048.1-5937 are very similar in nature to those observed in 4U0142+61. The implications of our observations for models of anomalous X-ray pulsars are discussed.