Purpose: Longitudinal studies to evaluate the effect of rehabilitative therapies require an objective, reproducible and quantitative means for testing function in vivo. An fMRI assessment tool for upper extremity related brain activation using an MRI-compatible manipulandum was developed and tested for use in neurorehabilitation research. Methods: Fifteen healthy, right-handed subjects participated in two fMRI sessions, which were three to four weeks apart. A block design paradigm, composed of three conditions of subject-passive movement, subject-active movement and rest, was employed for the fMRI recordings. During the rest condition, subjects simply held the device handle without applying any force or movement. The same type of auditory and visual instructions were given in all the three conditions, guiding the subjects to perform the motor tasks interactively with the MRI-compatible arm manipulandum. The tasks were controlled across the fMRI sessions. The subjects' brain activation was recorded by fMRI, and their behavioral performance was recorded by the manipulandum. The brain network activated by the subjects' interaction with the manipulandum was identified, and the reproducibility and reliability of the obtained activation were determined. Results: All subjects completed the trial protocol. Two subjects were excluded from analysis due to head motion artifacts. All passive movements were performed well. Four out of the total 780 active movements were missed by two subjects. Brain activation was found in the contralateral sensorimotor cortex, secondary somatosensory cortex and non-primary motor cortex as well as in subcortical areas in the thalamus, basal ganglia and the cerebellum. These activations were consistent across the two fMRI sessions. Conclusion: The MRI-compatible manipulandum elicited robust and reproducible brain activations in healthy subjects during the subject-active and subject-passive upper extremity motor tasks with a block design paradigm. This system is promising for many applications in neurorehabilitation research and may be useful for longitudinal studie