The objective of this study was to investigate the efficacy of an Electroencephalography (EEG)-based Motor Imagery (MI) Brain-Computer Interface (BCI) coupled with a Haptic Knob (HK) robot for arm rehabilitation in stroke patients. In this three-arm, single-blind, randomized controlled trial; 21 chronic hemiplegic stroke patients (Fugl-Meyer Motor Assessment (FMMA) score 10-50), recruited after pre-screening for MI BCI ability, were randomly allocated to BCI-HK, HK or Standard Arm Therapy (SAT) groups. All groups received 18 sessions of intervention over 6 weeks, 3 sessions per week, 90 minutes per session. The BCI-HK group received 1 hour of BCI coupled with HK intervention, and the HK group received 1 hour of HK intervention per session. Both BCI-HK and HK groups received 120 trials of robot-assisted hand grasping and knob manipulation followed by 30 minutes of therapist-assisted arm mobilization. The SAT group received 1.5 hours of therapist-assisted arm mobilization and forearm pronation-supination movements incorporating wrist control and grasp-release functions. In all, 14 males, 7 females, mean age 54.2 years, mean stroke duration 385.1 days, with baseline FMMA score 27.0 were recruited. The primary outcome measure was upper-extremity FMMA scores measured mid-intervention at week 3, end-intervention at week 6, and follow-up at weeks 12 and 24. Seven, 8 and 7 subjects underwent BCI-HK, HK and SAT interventions respectively. FMMA score improved in all groups, but no intergroup differences were found at any time points. Significantly larger motor gains were observed in the BCI-HK group compared to the SAT group at weeks 3, 12 and 24, but motor gains in the HK group did not differ from the SAT group at any time point. In conclusion, BCI-HK is effective, safe, and may have the potential for enhancing motor recovery in chronic stroke when combined with therapist-assisted arm mobilization.