Panax ginseng is being used for medicinal treatment and health tonic for over 2000 years in orient countries. As transplanting is necessary during ginseng cultivation, selection of ginseng seedling is of economic importance for ginseng production. The objective of this study was to determine the effects of seedling size on post-planting performance, yield and ginsenoside content. Ginseng seedlings from two cultivars (‘Kangmei01’ and ‘Xinkaihe01’) were classified into three grades, and a field experiment was carried out to investigate seedling performance of different grades in 2013–2015 and 2014–2016. Larger size ginseng seedlings generally had higher stem height, stem diameter and leaf area for all growth seasons, but the differences were not significant between adjacent grades sometimes. Larger size ginseng seedlings also resulted in greater main root length, root diameter, single root weight, yield and seed number per plant at harvest. In contrast, smaller size seedlings had higher increase index of single root weight and yield as well as higher ginsenoside content in main root at harvest. Different grades of ginseng seedlings did not show difference in survival rate at each growth season and rootlet ginsenoside content at harvest. The results suggested that larger ginseng seedlings had greater aerial part and gained higher yield, while smaller ones showed higher relative growth rate and contained larger amounts of ginsenosides.