We analyse the K2 short cadence data of the intermediate polar FO Aqr and provide accurate and updated orbital and spin periodicities. We additionally find small spin period changes as a function of orbital phase of ~0.02 seconds translating to velocities of ~ a few km/s. The obtained orbital-folded velocity profile displays two clear maxima and minima, and cannot be explained by the radial velocity of the orbiting white dwarf. Instead we propose that the observed velocities are the sum of the radial velocities of both the white dwarf and of the stellar surface facing the white dwarf which reprocesses the WD spin pulses. This combination can explain the observed low velocities in FO Aqr. However asymmetries in the orbital configuration are required to explain the double peaked velocity profile. One possible scenario would invoke binary eccentricity. We thus developed a simple binary model to explain and fit our observations, and find a small binary eccentricity of e=0.03. Although small, persistent eccentricity in a close interacting binary would induce enhanced mass transfer occurring preferentially at periastron passages. We thus discuss alternative scenarios where other asymmetries might explain our observations assuming circular orbits. Since FO Aqr is the first system where the combined radial velocities of both the WD and secondary surface have been measured, it is possible that other mass-transferring binaries also display similar velocity curves when observed with Kepler. These will provide additional valuable tests to either confirm or rule out small eccentricities in similar systems.
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