A system is provided for mounting at least one solar panel on a roof having standing seams protruding outwardly therefrom. The system may include a plurality of panel mounting brackets each comprising first and second flanges laterally spaced apart to define a seam channel therebetween, with the seam channel for receiving a given standing seam therein when the first and second flanges are positioned on the roof straddling the given standing seam. Each panel mounting bracket may also include a vertical extension portion carried by the first and second flanges. The system may further include a plurality of clamps each configured to couple the vertical extension portion of a respective panel mounting bracket with the at least one solar panel.