In the last decades, the tendon injuries have increased substantially. Previous results suggested that low-level laser treatment (LLLT) promotes synthesis of extracellular matrix and improves the functional properties of the tendon. The aim of this study was to evaluate the effects of different protocols of LLLT on partially tenotomized tendons. Adult male rats were divided into the following: G1-intact, G2-injured, G3-injured + LLLT (4 J/cm(2) continuous), G4-injured + LLLT (4 J/cm(2) at 20 Hz). G2, G3, and G4 were euthanized 8 days after injury. G5-injured, G6-injured + LLLT (4 J/cm(2) continuous), and G7-injured + LLL (4 J/cm(2) at 20 Hz until the seventh day and 2 kHz from 8 to 14 days). G5, G6, and G7 were euthanized on the 15th day. Glycosaminoglycan (GAG) level was quantified by dimethylmethylene blue method and analyzed on agarose gel. Toluidine blue (TB) stain was used to observe metachromasy. CatWalk system was used to evaluate gait recovery. Collagen organization was analyzed by polarization microscopy. The GAG level increased in all transected groups, except G5. In G6 and G7, there was a significant increase in GAG in relation to G5. In G3 and G4, the presence of dermatan sulfate band was more prominent than G2. TB stains showed intense metachromasy in the treated groups. Birefringence analysis showed improvement in collagen organization in G7. The gait was significantly improved in G7. In conclusion, pulsed LLLT leads to increased organization of collagen bundles and improved gait recovery.