The eccentric (ECC) exercises are an efficient way to exercise the muscles than concentric exercises. However, unaccustomed ECC may cause muscle damage, pain, delayed onset muscle soreness (DOMS) that may lead to temporary functional impairments. The aim is to measure the effects of performed yoga poses after various intensities of ECC exercise protocol with different ranges of motion (ROM) at the elbow and knee. Thirty-six participants aged between 18 and 30 years performed yoga after the ECC protocols (weeks 3, 5, 7, 9) and the ECC protocols without yoga poses (weeks 2, 4, 6, 8) on the elbow and knee muscles (5 × 10 repetitions each session) using their 25%/35% of maximal voluntary isometric contraction (MVIC). The subjective and objective assessments were carried out (activities of daily living (ADL), pain (visual analog scale (VAS), pain pressure threshold (PPT), and MVIC). The FROM ECC exercise with 35% of MVIC without yoga showed moderate pain (0-3.5) in ADL, VAS, and PPT for elbow extensors and showed a statistically significant difference (p ≤ 0.05) compared to the PROM ECC exercise with 25% of MVIC without yoga. ECC exercise performed with 35% of MVIC without yoga induced a higher degree of DOMS, pain, ADL limitations than 25% of MVIC without yoga. Yoga after PROM ECC protocol showed less pain, DOMS in VAS, and PPT for elbow flexors, knee flexors, and knee extensors. The overall percentage of increased MVIC value at the end of the study was between 30.53 and 43.12%. The upper extremity (extensors) muscles are more prone to DOMS and pain when compared to the lower extremity muscles. Performing yoga stretching poses after the eccentric exercise protocol may affect reducing DOMS and muscle pain.