Despite trans-tibial amputation being the most common major amputation, consensus on optimal stump management remains limited. Cohort studies comparing Ertl-tibiofibular synostosis (TFS) and Burgess-type stumps (BTS) have yielded conflicting results. We present the case of a bilateral trans-tibial amputee with a modified TFS on the right and a conventional BTS on the left. Instead of traditional myodesis, a myoplastic sling was created attaching residual tendons distal to the bone bridge to improve tendon sliding and perceptive feedback. Outcomes were assessed via load distribution, temporospatial gait analysis, adaptability tests, postural control studies, the Four Square Step Test (FSST), stair ascent, functional MRI, and tractography. The TFS stump appeared to show greater ambulation efficiency and was preferred during prolonged standing. FSST and circular gait tests revealed unsteadiness on the BTS side. No activated voxels appeared in the left postcentral gyrus during BTS loading. Movement of the TFS stump activated larger clusters in the contralateral precentral gyrus, while BTS movement activated the supplementary motor area. Fiber connections to the cerebellum via the superior cerebellar peduncle yielded more extensive streamline reconstructions during BTS movement. These unique trial conditions highlight subtle functional differences that are often missed in cohort studies but may significantly impact individual patient needs.