Purpose: Measurement of medial gastrocnemius (MG) tendon length using ultrasonography (US) requires the muscle–tendon junction (MTJ) to be located. Previously, the MG MTJ has been tracked from different proximo-distal locations near the MTJ, which could influence estimates of tendon length change due to the different characteristics of the aponeurosis and tendon. We used US to evaluate the effect of tracking point location on MG MTJ displacement during maximal and submaximal (10, 20 and 30% of the non-injured maximal) isometric plantar flexion contractions. Methods: Displacement behaviour of MTJ was tracked from (1) the exact MTJ; and (2) from an insertion point of a muscle fascicle on the aponeurosis 1.3 ± 0.6 cm proximal to the MTJ, in both limbs of patients with unilateral Achilles tendon rupture (ATR) (n = 22, 4 females, 42 ± 9 years, 177 ± 9 cm, 79 ± 10 kg). Results: In the non-injured limb, displacement (1.3 ± 0.5 cm vs. 1.1 ± 0.6 cm) and strain (6.7 ± 2.8% vs. 5.8 ± 3.3%) during maximal voluntary contraction were larger when tracking a point on the aponeurosis than when tracking the MTJ (both p < 0.001). The same was true for all contraction levels, and both limbs. Conclusion: Tracking a point on the aponeurosis consistently exaggerates estimates of tendon displacement, and the magnitude of this effect is contraction intensity-dependent. When quantifying displacement and strain of the Achilles tendon, the MTJ should be tracked directly, rather than tracking a surrogate point proximal to the MTJ. The latter method includes part of the aponeurosis, which due to its relative compliance, artificially increases estimates of MTJ displacement and strain.