Background In non-western countries, deep squatting is a daily activity, and prolonged deep squatting is common among occupational squatters. Household tasks, taking a bath, socializing, using toilets, and performing religious acts are among the activities frequently carried out while squatting by the Asian population. High knee loading is responsible for a knee injury and osteoarthritis. Finite element analysis is an effective tool to determine stresses on the knee joint. Methods Magnetic Resonance Imaging (MRI) and Computed Tomographic (CT) images were acquired of one adult without knee injuries. The CT images were acquired at the fully extended knee and one more set of images was acquired with the knee at a deeply flexed knee position. The MRI was acquired with the fully extended knee. 3-Dimensional models of bones were created using CT and soft tissue using MRI with the help of 3D Slicer software. Kinematics and finite element analysis of the knee was performed for standing and deep squatting posture using Ansys Workbench 2022. Results High peak stresses were observed at deep squatting compared to standing along with the reduction in the contact area. Peak von Mises stresses on femoral cartilage, tibial cartilage, patellar cartilage, and meniscus were increased from 3.3 MPa to 19.9 MPa, 2.9 MPa to 12.4 MPa, 1.5 MPa to 16.7 MPa and 15.8 MPa to 32.8 MPa respectively during deep squatting. Posterior translation of 7.01 mm, and 12.58 mm was observed for medial and lateral femoral condyle respectively from full extension to 153° knee flexion. Conclusions Increased stresses in the knee joint at deep squat posture may cause cartilage damage. A sustained deep squat posture should be avoided for healthy knee joints. More posterior translations of the medial femoral condyle at higher knee flexion angle warrant further investigation.