The dynamic enhancement pattern of HCCs smaller than 3 cm in diameter on gadoxetic acid-enhanced magnetic resonance imaging (MRI) have not been extensively investigated. We aimed to evaluate the dynamic enhancement patterns of small HCCs (≤3 cm) on gadoxetic acid-enhanced magnetic resonance imaging (MRI) and compare enhancement patterns with multiphasic multidetector computed tomography (MDCT) based on tumour cellular differentiation and size. We retrospectively included 55 patients with 67 surgically confirmed small HCCs (≤3 cm) who underwent multiphasic MDCT and gadoxetic acid-enhanced MRI. Dynamic enhancement patterns were analysed according to tumour cellular differentiation and size. Hepatobiliary phase images were also analysed to assess their additional value. The proportion of small HCCs demonstrating the typical enhancement pattern differed depending on tumour cellular differentiation on both MRI (P = 0.001) and MDCT (P = 0.001), but differed depending on tumour size only on CT (P = 0.008). Gadoxetic acid-enhanced MRI more sensitively depicted the typical enhancement pattern than CT for all tumours (P = 0.001), for moderately or poorly differentiated HCCs (P = 0.021) and for HCCs ≤2 cm (P = 0.001). 80% of tumours with atypical enhancement could be diagnosed as HCC based on tumour size and hepatobiliary phase images. On both gadoxetic acid-enhanced MRI and multiphasic CT, the dynamic enhancement patterns of small HCCs (≤3 cm) differed according to tumour cellular differentiation. Gadoxetic acid-enhanced MRI more frequently demonstrated the typical HCC enhancement pattern than CT in small HCCs.