A novel frequency-domain multiplexing system has been developed for in vivo measurements of rapid cerebral hemodynamics. The instrument operates in the frequency-domain with three optical wavelengths, six source positions, and two detectors. Frequency-division multiplexing was used to modulate three wavelengths (690, 786, and 830 nm) at slightly different frequencies around 70 MHz. The three laser output beams were combined and switched into different source positions by use of fast optical switches (switch time <10 ms). Three narrowband, in-phase and in-quadrature demodulators decode the modulated signals. Our full-frame-acquisition rate is 2.5 Hz, with flexibility for acquisition rates greater than 50 Hz with smaller detection areas. We evaluate the performance of the instrument with tissue phantoms, and then employ the system to measure in vivo cerebral blood oxygenation during forepaw stimulation of a rat’s brain.