The aim of the study was to assess the safety and effectiveness of stereotactic brain tumour biopsy (STx biopsy) guided by low-field intraoperative magnetic resonance imaging (iMRI) in comparison with its frameless classic analogue based on a prospective randomized trial. A pilot group of 42 brain tumour patients was prospectively randomized into a low-field iMRI group and a control group that underwent a frameless STx biopsy. The primary endpoints of the analysis were postoperative complication rate and diagnostic yield, and the secondary endpoints were length of hospital stay and duration of operation. The iMRI group (21 patients) and the control group (21 patients) did not differ significantly according to demographic and epidemiological data. No major postoperative complications were noted in either group. In addition, no significant differences in the diagnostic yield (p = 1.00) and length of hospital stay (p = 0.16) were observed. The mean total OR time was 111 ± 24 min in iMRI and 78 ± 29 min in the control group (p = 0.0001). Usage of iMRI may prolong the time of the procedure but seems to be comparable in safety and effectiveness to the standard frameless STx biopsy.