We performed a systematic review of the mechanisms of thyroid hormones (THs) associated with metabolic dysfunction associated with fatty liver disease (MAFLD). This systematic review was registered under PROSPERO (CRD42022323766). We searched the MEDLINE (via PubMed) and Embase databases from their inception to March 2022. We included studies that assessed thyroid function by measuring the serum level of THs and those involved in MAFLD. We excluded reviews, case reports, editorials, letters, duplicate studies and designed controls. Forty-three studies included MAFLD, eleven analyzed THs, and thirty-two evaluated the mechanisms of THs in MAFLD. Thyroid hormones are essential for healthy growth, development and tissue maintenance. In the liver, THs directly influence the regulation of lipid and carbohydrate metabolism, restoring the homeostatic state of the body. The selected studies showed an association of reduced levels of THs with the development and progression of MAFLD. In parallel, reduced levels of T3 have a negative impact on the activation of co-regulators in the liver, reducing the transcription of genes important in hepatic metabolism. Overall, this is the first review that systematically synthesizes studies focused on the mechanism of THs in the development and progression of MAFLD. The data generated in this systematic review strengthen knowledge of the impact of TH changes on the liver and direct new studies focusing on therapies that use these mechanisms.