Background <p>Many patients undergoing [¹⁸F] AlF-NOTA-FAPI-04 (¹⁸F-FAPI) PET/CT demonstrated diffuse thyroid uptake. These findings created challenges for accurate interpretation due to the limited understanding of physiological and non-oncologic causes of diffuse ¹⁸F-FAPI uptake in the thyroid. This retrospective study examined patients who underwent ¹⁸F-FAPI PET/CT imaging with diffuse thyroid uptake. It quantitatively assessed normal thyroid uptake, compared ¹⁸F-FAPI uptake between normal and diseased thyroids, and explored potential associations with diffuse thyroid uptake. The study may improve the accuracy of ¹⁸F-FAPI PET/CT interpretation for thyroid and facilitate appropriate management of diffuse thyroid uptake on ¹⁸F-FAPI PET/CT.</p> Results <p>A total of 38 patients were included in this study based on the inclusion criteria. The mean SUVmax, SUVmean, and TBR of normal thyroid were 7.09 ± 3.83, 4.24 ± 2.25 and 3.93 ± 1.73, respectively. Quantitative analysis revealed no significant asymmetry in ¹⁸F-FAPI uptake between the right and left thyroid lobes (SUVmax: right 6.69 ± 2.96 vs. left 6.54 ± 3.28, <i>p</i> = 0.84; SUVmean: right 4.19 ± 1.73 vs. left 4.18 ± 1.97, <i>p</i> = 0.98), consistent with the diffuse uptake pattern observed. There was no significant correlation between Hashimoto thyroiditis, serum TSH levels, and the degree of diffuse thyroid uptake (all <i>p</i> &gt; 0.05 for SUVmax, SUVmean, and TBR). Furthermore, no association was observed between sex, age, immunotherapy, and diffuse thyroid uptake (<i>p</i> &gt; 0.05).</p> Conclusions <p>Diffuse uptake of ¹⁸F-FAPI in the thyroid may not significantly relate to Hashimoto thyroiditis or abnormal serum TSH levels. Lesions on ¹⁸F-FAPI PET/CT scans might be hard to detect due to the moderate uptake in normal thyroid tissue.</p>