We present an instrument for simultaneous imaging of the rodent brain with frequency-domain optical tomography and magnetic resonance imaging. The instrument uses a custom-built fiber optic probe that allows for measurements in backreflectance geometry. The probe consists of 13 source and 26 detector fibers and is small enough to fit inside of a microMRI RF coil with an inner diameter of 38mm. Illumination by the source fibers is time demultiplexed by an optical fiber switch. A gain-modulated image intensifier CCD camera focuses onto the endpoints of large-core gradedindex detector fibers and collects the frequency-domain data. Imaging can be performed with source-modulation frequencies up to 1 GHz. The instrument is capable of acquiring multi-frequency optical tomography data at 2 wavelengths, and the data can be used to generate 3D maps of hemoglobin concentrations. At the same time magnetic resonance images can be acquired with in-plane resolution smaller than 100 micron. To illustrate the performance of the instrument we show results of small animal studies that involve inhalation of 100% carbogen and chemically induced seizures.