SET and MYND domain-containing protein 3 (SMYD3), a histone methyltransferase, plays a key function in the progression of human cancer. However, the role of SMYD3 in gastric carcinoma carcinogenesis has yet to be elucidated. This study aimed to determine the relationships of SMYD3 expression with clinicopathological characteristics and prognosis in gastric carcinoma. The expression of SMYD3 was detected by real-time quantitative reverse transcription PCR and Western blot in gastric carcinoma (GC) cell lines, normal gastric mucosa cell line, GC tissues, and adjacent non-tumor tissues. SMYD3 expression in tissue sections of 180 gastric carcinoma samples were evaluated using immunohistochemistry. The staining results were compared with clinicopathological characteristics and to the outcome of patients. The expression levels of SMYD3 messenger RNA (mRNA) and protein in GC tissues were both higher than those in adjacent non-tumor tissues (p < 0.05). SMYD3 mRNA and protein expression levels were higher in GC cell lines MKN28, SGC7901, and MGC803 than normal gastric mucosa cell line GES-1. SMYD3 expression in gastric carcinoma was significantly correlated with primary tumor size (p < 0.001), lymph node metastasis (p < 0.001), and TNM stage (p = 0.011). Degree of differentiation [hazard ratio (HR) = 5.113; p = 0.006], serosal invasion (HR = 2.074; p = 0.024), lymph node metastasis (HR = 1.354; p < 0.001), and SMYD3 expression (HR = 0.564; p = 0.004) were identified as the independent factors of the overall survival (OS) in all enrolled GC patients. For patients with positive lymph node metastasis, degree of differentiation (HR = 5.974; p = 0.015), lymph node metastasis (HR = 1.257; p < 0.001), and SMYD3 expression (HR = 0.529; p = 0.004) were the independent prognostic factors of the OS. SMYD3 performed an important function in the aggressiveness of gastric carcinoma and may act as a promising target for prognostic prediction.