This study aimed to compare the effects of low- and medium-frequency NMES, combined with a standard physical therapy (SPT) program, on functional capacity in critically ill patients. Fifty-four critically ill patients admitted into Intensive Care Unit (ICU) and on mechanical ventilation participated in this randomized, single-blinded, experimental study. Participants were randomly assigned to a Control group, who received a lower limb SPT program; the Low-frequency NMES group received lower limb SPT + NMES at 100 Hz; and the Medium-frequency NMES group received lower limb SPT + NMES at 100 Hz with a carrier frequency of 2500 Hz. The outcomes, encompassing functional capacity in the hospital, included muscle strength, handgrip strength, functional status, degree of independence for activities of daily living, functional and dynamic mobility, quality of life, and total days hospitalized. Both NMES protocols combined with SPT improved functional capacity compared to the control group. Medium-frequency NMES provided additional benefits on dynamic balance, in the degree of independence to perform activities of daily living and quality of life (all < 0.001) prior to hospital discharge. It also promoted larger gains on functional status prior to ICU discharge and on knee extension strength (both < 0.05) prior to intermediate care unit discharge. Medium-frequency NMES also enhanced handgrip strength earlier than low-frequency NMES when compared to the control group. Notably, medium-frequency NMES was the only intervention associated with a significant reduction in total hospital stay duration ( < 0.05). Medium-frequency NMES, along with an SPT program in critically ill patients, showed greater benefits on functional capacity during recovery than low-frequency NMES. (Trial registration: This trial is registered on ClinicalTrials.gov: NCT05287919). 1. Medium-frequency NMES may enhance physical functionality and quality of life in critically ill patients with ICU-acquired weakness. 2. Medium-frequency NMES can reduce the number of hospitalization days. 3. NMES combined with SPT represents a feasible and effective option for patients unable to engage in active rehabilitation during critical illness.