We present a novel pilot-point-based hydraulic tomography (HT) inversion procedure to delineate preferential flow paths and estimate hydraulic properties in a fractured aquifer. Our procedure considers a binary prior model developed using a randomized algorithm. The randomized algorithm involves discretizing the domain into grid cells, assigning a binary label to each cell, traversing the grid randomly, and choosing the optimal grid configuration cell-by-cell. This binary prior model is used to guide the placement of pilot points and to constrain aquifer parameters during pilot-point-based HT inversion. A two-dimensional fractured granite rock block was considered to test our methodology under controlled laboratory conditions. Multiple pumping tests were conducted at selected ports and the pressure responses were monitored. The pumping datasets thus obtained were preprocessed using median filters to remove random noise, and then analyzed using the proposed procedure. The proposed binary prior algorithm was implemented in C++ by supplying the forward groundwater model, HydroGeoSphere (HGS). Pilot-point-assisted HT inversion was performed using the parameter-estimation tool, coupled to HGS. The resulting parameter distributions were assessed by: (1) a visual comparison of the K- and Ss -tomograms with the known topology of the fractures and (2) comparing model predictions with measurements made at two validation ports that were not used in calibration. The performance assessment revealed that HT with the proposed randomized binary prior could be used to recover fracture-connectivity and to predict drawdowns in fractured aquifers with reasonable accuracy, when compared to a conventional pilot-point inversion scheme.