The treatment of brain arteriovenous malformations supplied by deep perforating arteries (PA) (P-BAVM) remains challenging. The aims of this study were to determine the outcomes after surgical treatment in patients with P-BAVMs and to identify the risk factors associated with postoperative neurological deficits. We retrospectively reviewed the medical charts and imaging records of 228 consecutive patients with BAVMs who underwent microsurgical resection of their BAVMs at Beijing Tiantan Hospital between September 2012 and March 2016. Patients were included if the BAVMs were totally or partially supplied by PA. All patients had undergone preoperative diffusion tensor imaging (DTI), MRI, 3D time-of-flight MRA (3D TOF-MRA) and digital subtraction angiography (DSA) followed by resection. Both functional and angioarchitectural factors were analysed with respect to the postoperative neurological deficits, including motor deficits, visual field deficits and aphasia. Statistical analysis was performed using the statistical package SPSS (version 20.0.0, IBM Corp.). Fifty-nine patients with P-BAVMs were enrolled. Radical obliteration was achieved in all P-BAVMs according to postoperative DSA. Forty-five (76.3%) patients obtained neurological deficits 1 week after surgery. At a mean follow-up of 14.7 ± 9.4 (3–30) months after surgery, 34 patients (57.6%) had long-term neurological deficits. Multivariable logistic regression analyses showed that a shorter lesion-to-eloquent fibre tracts distance (LFD) was an independent risk factor for short- (P = 0.014) and long-term (P = 0.013) neurological deficits. The cut-off point of LFD for long-term neurological deficits was 5.20 mm. The predominant supply of the PA (P = 0.008) was an independent risk factor for long-term neurological deficits. This study identified a high risk of surgical morbidity for P-BAVMs. The predominant supply of the PA and a shorter LFD are crucial risk factors for postoperative neurological deficits in patients with P-BAVMs.