Neuronal development can be severely impacted under pathological conditions, altering the maturation of neuronal cells. Allan Herndon Dudley Syndrome (AHDS) is a rare X-linked syndrome caused by a mutation in the SLC16A2 gene, which encodes the specific transporter (monocarboxylate transported 8, MCT8) of thyroid T3 hormone, reducing its presence in the central nervous system and leading to severe neurological impairment. We investigated the neuronal maturation in an in vitro organoid model of AHDS, in which the pathological condition was resembled by removing the T3 hormone from the culture media. A bulk RNA sequencing analysis was performed at different stages of the organoid development (7 and 14 days in vitro). Transcriptome analysis revealed that, compared to control, AHDS organoids up-regulated pathways related to stemness and proliferation (e.g., DNA replication, mRNA transport, and protein folding) and down-regulated pathways related to fatty acid metabolism, synaptic transmission, neuronal action potential, and mitochondrial structures. Evolutionary transcriptome analysis was then performed to monitor the organoid’s development from day 7 to day 14. While control organoids show an up-regulation of pathways involved in the neurodevelopment (e.g., neuron differentiation and neuron projection development), AHDS organoids positively regulate pathways related to the maintenance of stemness and to astrocyte differentiation (e.g., regulation of the Notch signaling pathway). Still, impairment in neurodevelopment was paired with progressive downregulation of pathways related to mitochondrial activity in AHDS. Overall, this study highlighted -omics analysis as a tool to reveal the pivotal role of the T3 hormone during neuronal development in AHDS.