Equine subchondral bone cysts (SBCs) develop most often in the medial femoral condyle (MFC) of yearlings intended for performance. SBCs often cause lameness and can cause secondary injuries to the meniscus and tibial cartilage. A novel surgical technique using a transcondylar lag screw (TLS) across an MFC SBC has shown success in lameness resolution and radiographic healing of MFC SBC. In a previous study using finite element analysis, our lab showed that a TLS stimulated bone formation on the inner surface of the SBC and altered third principal stress vectors to change the direction of surface compression to align with the screw axis. This work extended the previous study, which was limited by the use of only one idealized SBC. Our objective was to test SBCs of several sizes and shapes in a newly developed equine stifle FEM with a TLS to determine how cyst size affects bone formation stimulation. This study found that a transcondylar screw is most effective in stimulating bone formation in cysts of greater height (proximal-distal). The TLS increases stress stimulus in the bone around the cyst to promote bone apposition and directs compression across the cyst. If full penetration of the screw through the cyst is possible, it is recommended that the transcondylar screw be used to treat subchondral bone cysts. For the treatment of smaller cysts that are not accessible by the current screw surgical approach, future work could study efficacy of a dual-pitch headless screw that that may reach smaller cysts.