Pc3 pulsations are observed in the magnetosphere with wave periods of 10–45 s. Two distinct populations have been observed; one exhibits a frequency dependence on the solar wind magnetic field strength, whereas the other does not. The first population is explained in terms of a model where the bow shock reflects ions which generate upstream foreshock ULF waves. These waves are convected through the shock to the dayside magnetopause and thus to the magnetosphere. The source of the second population is not well understood. In this paper we examine the generation of a transient patch of Pc3 wave activity due to a hot flow anomaly (HFA) using a unique spacecraft conjunction that occurred during the first Earth flyby of the Rosetta spacecraft. Cluster, upstream of the bow shock and close to the Sun-Earth line observed an HFA. At this time Rosetta was nearing closest approach and together with ground magnetometer stations, observed a transient interval of Pc3 wave activity. Analysis also shows that the Pc3 waves occurred in the absence of a ULF wavefield just upstream of the bow shock. This result shows that HFAs can be a source of Pc3 wave activity, and may explain in part the origin of the second population of Pc3 waves. It also demonstrates in new detail the manner in which kinetic physics at the bow shock, driven by structure in the solar wind, can influence magnetospheric dynamics.