Akt signaling is an important regulator of neural development, but the distinctive function of Akt isoforms in the brain development presents a challenge. Here we show Siah1 as an ubiquitin ligase that preferentially interacts with Akt3 and facilitates ubiquitination and degradation of Akt3. Akt3 is enriched in axonal shaft and branches but not growth cone tips where Siah1 is prominently present. Depletion of Siah1 enhanced Akt3 levels in the soma and axonal tips, eliciting multiple branching. Brain specific somatic mutation in Akt3-E17K escapes from Siah1 mediated degradation and causes improper neural development with dysmorphic neurons. Remarkably, coexpression of Siah1 with Akt3-WT restricted disorganization of neural development caused by Akt3 overexpression whereas the forced expression of Siah1 with Akt3-E17K mutant fails to cope the malformation of neural development. These findings demonstrate that Siah1 limited Akt3 turnover during brain development and this event is essential for normal organization of neural network.