Boron-based rods are ideal for remedial treatments in wood attacked by decay fungi, insects and termites as well as for preventive treatments of high-risk areas in structural timbers and logs internally. This study evaluated the solubility, some physical and thermal properties of the boron-based rods manufactured from either raw ulexite mineral, raw colemanite mineral, di-sodium octaborate tetrahydrate (DOT), and their combination of silica-based plasticizer. This is the first attempt to produce ulexite and colemanite-based boron rods with/without additional compound by an extruder. To take the advantages of boron minerals, rods were produced with paste mixtures of boron compounds and plasticizer by a single-screw extrusion method. Solubility and thermal resistance tests as well as micro-hardness tests were performed to determine the quality and strength of the rods for discussing the on-site applications. The paste content was an important factor affecting the transport processes during single screw extrusion with special emphasis on the rod formation. No macro-structural changes were observed when the boron rods were exposed to heat at 30, 50, 70, 100, and 200 °C. According to the Kruskal–Wallis test, no significant difference was observed in micro-hardness values of thermally treated boron-based rods; however, at high temperatures up to 50 °C, there was a decrease in hardness of DOT rods. The rods manufactured by extrusion methods showed similar water solubility when compared to raw ulexite and colemanite minerals.