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Background: Patellofemoral pain (PFP) often affects young women, and the etiology is multifactorial and poorly understood. Conservative intervention has been focused on risk factors or aggravating factors and is composed of hip- and knee-strengthening exercises, as this population often has muscle weakness and poor motor control during daily and sports activities. The objective of this study was to evaluate the additional effects of neuromuscular training in a conservative treatment of trunk-, hip-, and knee-muscle strengthening on pain, function, and kinematics of the trunk, pelvis, and lower limb in women with PFP., Methods: This is a randomised clinical trial, controlled, blinded. Ninety women who are active and engage in physical activity up to twice a week will be recruited. All participants will undergo an individual physiotherapy assessment and then will be allocated randomly into two groups. Thereafter, both groups will undergo a 12-week intervention protocol: group 1 will perform strengthening exercises for the trunk, hip, and knee muscles, while group 2 will receive the same treatment, with the inclusion of neuromuscular training exercises on the fourth week. At the end of the intervention, the volunteers will be evaluated. The primary outcomes will be pain intensity (using a Visual Analog Scale: over the last month, squat 90°, and step of 26 cm during 1 min), functional capacity (Anterior Knee Pain Scale and Activities of Daily Living Scale), and 2D kinematics of the trunk, pelvis, and lower limb during the single-leg squat. The secondary outcomes correspond to the isometric muscular strength of the lower limb and the level of satisfaction from the intervention., Discussion: The present study was initiated on 28 January 2018 and is currently in progress, scheduled for completion in July 2019. The results of this study should contribute to the physiotherapeutic treatment of women with PFP by aggregating information on the benefits of adding neuromuscular training to strengthening of the trunk and lower-limb muscles., Trial Registration: Registro Brasileiro de Ensaios Clínicos, ID: RBR-8c7267 . Registered on 2 August 2017.