Objective: This study aimed to assess the relative and absolute intra- and inter-rater reliability of supraspinatus tendon (SST) thickness. Materials: Thirty adolescent swimmers with supraspinatus (SS) tendinopathy (n = 15) and a control-matched group (n = 15) were evaluated. Tendon thickness was measured according to four different measure procedures, i.e., (1) at 15 mm, (2) at 10, 20, and 30 mm, (3) at 10, 15, and 20 mm, and (4) 5 and 10 mm lateral to the most hyperechogenic reference point of the biceps tendon. Each examiner took two US images for the test measurements with a 10 min rest period. After 30 min, the subjects underwent retest measurements that were also repeated 1 week later. Results: SST thickness was greater in swimmers with SS tendinopathy compared with the matched control group for each procedure and rater (p < 0.001). Intra- and inter-rater reliability was good to excellent (ICC2.3: 0.78-0.98 and 0.83-0.97, respectively) in both groups. The lowest intra- and inter-rater reliability was found in procedures no. 2 and 4 (ICC2.3: 0.78 and 0.83). However, procedure no. 3 was the most reliable with the lowest error rate (ICC2.3: 0.92-0.97; SEM: 0.05-0.10 mm; MDC: 0.14-0.28 mm). Conclusions: The study confirmed the diagnostic value of ultrasound in SS tendinopathy. A multiple-reference-point procedure including a simple methodology (10, 15, and 20 mm from biceps tendon), was defined as the most reliable, expressed by the highest intra- and inter-rater ICCs.