Mitochondria play essential metabolic roles and are increasingly understood to interact with other organelles, influencing cellular function and disease. Primary cilia, as sensory and signalling organelles, are crucial for neuronal communication and function. Emerging evidence suggests that mitochondria and primary cilia may interact to regulate cellular processes, as recently shown in brain cells such as astrocytes. Here, we investigated whether mitochondria also regulate primary cilia in neurons, focusing on molecular pathways linking both organelles and structural components within cilia. We employed a cross-species, molecular pathway-focused approach to explore connections between mitochondrial and ciliary pathways in neurons, revealing strong associations suggesting coordinated functionality. Furthermore, we found that viral-induced downregulation of the mitochondrial fusion gene mitofusin 2 (Mfn2) in dopamine D1 receptor-expressing medium spiny neurons (D1-MSNs) of the nucleus accumbens (NAc) altered ciliary gene expression, with Crocc - the gene encoding rootletin - showing the most pronounced downregulation. This reduction in Crocc expression was linked to decreased levels of rootletin protein, a key structural component of the ciliary rootlet. Notably, viral-mediated overexpression of rootletin restored ciliary complexity and elongation, without compromising neuronal adaptation to Mfn2 downregulation. Our findings provide novel evidence of a functional mitochondria-cilia interaction in neurons, specifically in striatal D1-MSNs. These results reveal a previously unrecognized role of mitochondrial dynamics in regulating ciliary structure in neurons, with potential implications for neuropsychiatric and neurodegenerative disease mechanisms.