Repetitive transcranial magnetic stimulation (rTMS) is a promising approach for post-stroke rehabilitation but there lacks a rationale strategy to plan, execute, and monitor treatment. We present a case of targeted rTMS using the Omniscient Infinitome software to devise targets for treatment in a post-stroke patient and describe the functional connectomic changes after treatment. A 19-year-old female with no medical history presented 19 months after suffering a left middle cerebral artery (MCA) superior division ischemic stroke, resulting in language impairment and diminished right upper extremity motor function. She underwent a resting-state MRI (rsMRI) with tractography and images were processed using the Omniscient Infinitome software. Analysis using the anomaly detection within the software enabled us to identify three targets for rTMS (left area 1, left area 45, and right area SFL). These areas were treated with 25 sessions of intermittent Theta Burst Stimulation (iTBS) over five days at 80% of motor threshold concomitantly with targeted physical therapy and speech therapy. At five months follow-up, her language and right upper extremity functions significantly improved. Her connectomic analysis revealed substantial neural changes, including normalization of the sensorimotor network, substantially thicker callosal fiber bundle connecting the two hemispheres, and increased cortical recruitment in her language network. We present the first description of robust connectomic alterations in a post-stroke patient following targeted rTMS treatment. Further studies on the use of rTMS with an emphasis on functional connectomics are warranted.