There is a need for clinical indicators that can be used to guide the treatment of Achilles tendon complaints in recreational runners. Diagnostic ultrasound has recently been introduced for clinical decision support in tendon pain management. The aim of this study was to determine whether tendon thickness and morphological changes in the Achilles tendon detected in ultrasound examinations are associated with local symptoms in middle-age recreational long-distance runners. Forty-two Achilles tendons (21 middle-aged runners) were investigated by ultrasound examination measuring tendon thickness and a morphology score indicating tendinosis. The Generalized Estimating Equations method was applied in multiple models of factors associated with reporting a symptomatic tendon. Eleven symptomatic and 31 asymptomatic Achilles tendons were recorded. In the multiple model that used tendon thickness measured 30 mm proximal to the distal insertion, an association was found between thickness and reporting a symptomatic tendon (p < 0.001; OR 12.9; 95% CI 3.1 to 53.2). A qualitative morphology score was not found to be significantly associated with reporting a symptomatic tendon (p = 0.10). We conclude that symptomatic Achilles tendons were thicker than asymptomatic tendons on ultrasound examination among recreational long-distance runners and that the importance of parallel morphological findings need to be further investigated in prospective studies.