Nutritional assessment is essential to identify patients with acute kidney injury (AKI) who are protein-energy wasting (PEW) and at risk of poor clinical outcomes. This systematic review aimed to investigate the relationship of nutritional assessments for PEW with clinical outcomes in patients with AKI. A systematic search was performed in PubMed, Scopus, and Cochrane Library databases using search terms related to PEW, nutrition assessment, and AKI to identify prospective cohort studies that involved AKI adult patients with at least one nutritional assessment performed and reported relevant clinical outcomes, such as mortality, length of stay, and renal outcomes associated with the nutritional parameters. Seventeen studies reporting eight nutritional parameters for PEW assessment were identified and mortality was the main clinical outcome reported. A meta-analysis showed that PEW assessed using subjective global assessment (SGA) was associated with greater mortality risk (RR: 1.99, 95% CI: 1.36–2.91). Individual nutrition parameters, such as serum chemistry, body mass, muscle mass, and dietary intakes, were not consistently associated with mortality. In conclusion, SGA is a valid tool for PEW assessment in patients with AKI, while other nutrition parameters in isolation had limited validity for PEW assessment.