Pulsar timing has enabled some of the strongest tests of fundamental physics. Central to the technique is the assumption that the detected radio pulses can be used to accurately measure the rotation of the pulsar. Here we report on a broad-band variation in the pulse profile of the millisecond pulsar J1643-1224. A new component of emission suddenly appears in the pulse profile, decays over 4 months, and results in a permanently modified pulse shape. Profile variations such as these may be the origin of timing noise observed in other millisecond pulsars. The sensitivity of pulsar-timing observations to gravitational radiation can be increased by accounting for this variability.