Purpose: Prostate imaging to guide biopsy remains unsatisfactory, with current solutions suffering from high complexity and poor accuracy and reliability. One novel entrant into this field is micro-ultrasound (microUS), which uses a high frequency imaging probe to achieve very high spatial resolution, and achieves prostate cancer detection rates equivalent to multiparametric magnetic resonance imaging (mpMRI). However, the ExactVu transrectal microUS probe has a unique geometry that makes it challenging to acquire controlled, repeatable three-dimensional (3D) transrectal ultrasound (TRUS) volumes. We describe the design, fabrication, and validation of a 3D acquisition system that allows for the accurate use of the ExactVu microUS device for volumetric prostate imaging. Methods: The design uses a motorized, computer-controlled brachytherapy stepper to rotate the ExactVu transducer about its axis. We carry geometric validation using a phantom with known dimensions and we compare performance with magnetic resonance imaging (MRI) using a commercial quality assurance anthropomorphic prostate phantom. Results: Our geometric validation shows accuracy of 1 mm or less in all three directions, and images of an anthropomorphic phantom qualitatively match those acquired using MRI and show good agreement quantitatively. Conclusion: We describe the first system to acquire robotically-controlled 3D microUS images using the ExactVu microUS system. The reconstructed 3D microUS images are accurate, which will allow for applications of the ExactVu microUS system in prostate specimen and in vivo imaging.