Introduction High false-negative results have been reported for fine-needle aspiration (FNA) cytology in thyroid nodules. Fine-needle capillary (FNC) cytology is an alternative technique that prevents aspiration, reducing tissue damage. This study aimed to compare FNA and FNC in assessing thyroid nodules and in terms of their predictive role in the appropriate diagnosis of malignancy. Methods This is a comparative prospective study conducted on 486 patients. FNA was performed in 235 patients during 2016 and 2017 and FNC in 251 patients during 2018 and 2019. The quality of cytological specimens was compared and then correlated with the final histopathological findings of 39 patients who underwent thyroidectomy. Results Both groups were statistically similar regarding age and sex distribution. The FNA technique yielded significantly higher adequate specimens compared with FNC (p<0.001). Abundant blood in the background was found more frequently in the FNA technique (p<0.001). The sensitivity and specificity of FNA for malignancy diagnosis were both 100%, compared with 83.3% and 57.7% for FNC, respectively. Conclusions The two methods, FNA and FNC, did not differ in terms of overall quality. FNA was superior regarding consistency with the histopathological results and the ability to diagnose malignancy.