Lymphatic metastasis is a primary cause of gastric cancer-related death, yet factors governing tumor cell lymphatic metastasis have not been fully elucidated. Little is known about the contributions of long noncoding RNAs (lncRNAs) to lymphatic metastasis in gastric cancer. Differentially expressional lncRNAs between metastatic lymph node tissues and normal lymph node tissues were identified and validated by microarray and quantitative real-time polymerase chain reaction (qRT-PCR), respectively. Our results found that the expression level of C21orF96 was over-expressed in positive lymph node tissues and gastric cancer tissues. We evaluated the altered expressions of C21orF96 in gastric cancer tissues comparing to adjacent normal specimens, and their association with clinicopathological factors. We showed that the expression levels of C21orF96 were associated with gross appearance, lymphatic metastasis and distal metastasis. The effect of C21orF96 was assessed by over-expressing the lncRNA. We also found that C21orF96 promoted the tubular formation, migration and invasion. Together, our results suggest that C21orF96 is an oncogenic lncRNA that promotes tumor progression and plays a pivotal role in the development of gastric cancer.