Purpose Microfractures at the footprint may be a potential additional source of growth factor and enhance the tendon healing at the bone-tendon junction when repairing rotator cuff tears. Methods Fifty-seven patients who underwent shoulder arthroscopy for repair of complete rotator cuff tears were randomly divided into two groups, using a block randomisation procedure. Patients underwent microfracture at the footprint in the treatment group. The patients in the control group (n=29) did not receive that treatment. All patients had the same post-operative rehabilitation protocol. Results The two groups were homogeneous. There was a significant improvement from baseline to the last minimum follow-up of two years. At three months from the index procedure, visual analogue scale (VAS), range of motion (ROM) and University of California at Los Angeles (UCLA) and Constant scores were significantly better in group 1 than in group 2 (P<.05). At the last follow-up (minimum two years), clinical and functional outcomes were further improved in both the groups but inter-group differences were not significant. No technique-related complications were recorded. Conclusions Microfractures at the footprint are simple, safe, inexpensive and effective at producing less pain in the short term in patients who undergo rotator cuff repair, but at two years they do not result in significantly different outcomes, either clinically or at imaging, compared to traditional rotator cuff repair.