Introduction: Apelin could be one of the last protective defenses before developing obesity-related disorders, including insulin resistance, type 2 diabetes, and hypertension, which can be modified by dietary intake. The present study investigated the association of habitual intake of total fatty acids (TFAs), saturated-, monounsaturated-, polyunsaturated FAs, n-3, and n-6 FAs with Apelin expression in visceral adipose tissue (VAT) and subcutaneous adipose tissue (SAT). Methods: We obtained VAT and SAT from 168 participants (64 nonobese and 104 obese) who had undergone open abdominal surgery. Dietary intake information was gathered with a valid and reliable food frequency questionnaire. The mRNA expression of the Apelin gene was analyzed by real-time PCR. Results: Apelin serum levels were increased in the obese subjects compared to the nonobese group (p = 0.016). The SAT and VAT Apelin mRNA levels were significantly elevated in the obese participants compared to the nonobese ones (p < 0.05). Based on BMI status, only obese subjects indicated a positive association between SAT and VAT Apelin expression and TFA intake (p < 0.001). However, this association was observed between SAT and VAT Apelin gene expression and polyunsaturated fatty acid (PUFA) and n-3 FA intakes in both obese and nonobese groups (p < 0.05). Conclusion: High Apelin gene expression was associated with TFA intake in obese subjects in both fat tissues. However, habitual intake of PUFA and n-3 FA was associated with Apelin gene expression in obese and nonobese individuals. Our results indicate a determinative role of the quality and quantity of FA intake on adipose tissue.