Background: Studies have demonstrated that a sub-group of patients with medial Achilles pain exhibit Achilles tendinopathy with plantaris tendon involvement. This clinical condition is characterised by structural relationships and functional interference between the two tendons, resulting in compressive or shearing forces. Surgical plantaris tendon removal together with an Achilles scraping procedure has demonstrated positive short-term clinical results. The aim of this case series was to determine the long-term outcomes on pain and Achilles tendon structure. Methods: 18 consecutive patients (13 males; 5 females; mean age 39 years; mean symptom duration 28 months), of which three were elites, were included. Clinical examination, b-mode ultrasound (US) and Ultrasound Tissue Characterisation (UTC) confirmed medial Achilles tendon pain and tenderness, medial Achilles tendinopathy plus a plantaris tendon located close to the medial side of the Achilles tendon. Patients underwent US-guided local Achilles scraping and plantaris tendon removal followed by a structured rehabilitation program. Outcomes were VISA-A score for pain and function and UTC for Achilles structure. Results: 16 of 18 patients completed the 24 months follow-up. Mean VISA-A scores increased from 58.2 (±15.9) to 92.0 (±9.2) (mean difference = 33.8, 95% CI 25.2, 42.8, p < 0.01). There was an improvement in Achilles structure with mean organised echo pixels (UTC type I+II, in %) increasing from 79.9 (±11.5) to 86.4 (±10.0) (mean difference = 6.5%, 95% CI 0.80, 13.80, p =0.01), exceeding the 3.4% minimum detectable change. All 16 patients reported satisfaction with the procedure and 14 returned to pre-injury activity levels. There were no reported complications. Conclusions: Improved pain, function and tendon structure were observed 24 months after treatment with Achilles scraping and plantaris excision. The improvement in structure on the medial side of the Achilles after plantaris removal indicates that compression from the plantaris tendon might be an important presenting factor in this sub-group.