Bcl-2-associated athanogene (BAG) 3 is known as a regulator of cell death as well as autophagic protein turnover in the heart. However, little information is present in functional role of BAG3 in neurons. We analyzed the functional role of BAG3 in N1E115 cells derived from mouse neuroblastoma. While overexpression of Bcl-xL, a member of anti-apoptotic factor, can prevent cell death against 30 nM staurosporine, no obvious protective effect was seen by overexpression of BAG3 in N1E115 cells. In contrast, combined overexpression of BAG3 with Bcl-xL can enhanced the effect by overexpression of Bcl-xL in N1E115 cells. Slight protective effect of BAG3 against ABT263, Bcl-2 inhibitor, was also observed in N1E115 cells. To address underlying mechanisms of protective effect of BAG3, overexpression as well as knockdown of BAG3 was performed. Although knockdown of BAG3 in N1E115 cells using si-RNA specifically targeted to BAG3 enhanced mitochondrial Bak1 protein levels, no alteration in Bak1 gene expression, and gene expression and protein levels of Bax, Bcl-2 was observed. Concomitant with increased Bak1, the proportion of TUNEL-positive N1E115 cells was increased, and overexpression of BAG3 led to suppression of the Bak1 level. Bafilomycin A1, an autophagy inhibitor, can inhibit the modification of Bak1 protein level by BAG3. These results suggest that BAG3 may be critical to protein level in Bak1 via modification of autophagy activity, and that autophagy regulation by BAG3 may play an important role in the apoptosis of neuronal cells.