The presence or absence of magma exerts a fundamental control on the distribution of strain in continental rift zones, yet the time scales of magma intrusion remain unconstrained. Using more than a decade of measurements from interferometric synthetic aperture radar (InSAR), we detected geodetic activity at four of the eleven central rift volcanoes in the Kenyan sector of the East African Rift. Subsidence of 2–5 cm occurred at Suswa and Menengai over the period 1997–2000, ~9 cm of uplift was recorded at Longonot in 2004–2006, and ~21 cm of uplift occurred at Paka during 2006–2007. The deformation is episodic, and no deformation was observed at these volcanoes during other time periods. Preceding the inflation at Paka, we observed transient uplift and subsidence of a second, nearby source, likely associated with flow through a complex plumbing system. The best-fitting source models for each episode include inflation or deflation of a horizontal penny-shaped crack at a depth of 2–5 km. The episodic nature of the activity, its lack of correlation with seasons, and the preferred source geometry are all consistent with activity in the volatile-rich cap to a crystal-rich magma chamber beneath each of the four volcanoes. The presence of active magmatic systems beneath more than 40% of the volcanoes, and the 2007–2008 explosive eruptions at nearby Oldoinyo Lengai volcano, have implications for models of continental rifting, caldera volcanoes, geothermal resources, and volcanic and seismic hazard in rift zones.