Several tyrosine phosphatases control cell motility; understanding their signaling helps to decipher cancer mechanisms. Previously, we found that the negative regulation of migration exerted by PTPN12 in ovarian cancer SKOV-3 cells involves direct FAK Y397 targeting, in HER2-dependent way. In this study, we describe that PTPN12 silencing depresses also PTEN RNA and protein. This, in turn, contributes to regulate FAK, through the activation of the PI3K/AKT pathway, resulting in GSK3 inactivation and decreased FAK phosphorylation at the inhibitory and GSK3 target S722. Altogether, in SKOV-3 cells, both PTPN12 and PTEN signaling merge on FAK which is negatively regulated through Y397 dephosphorylation (directly by PTPN12) and S722 phosphorylation (through PTEN/AKT/GSK3). Although HER2 activity sustains SKOV-3 cell motility, the HER2 inhibitor Ag825 impairs migration only in PTPN12 silenced cells, suggesting the ability of PTPN12 to affect HER2. This hypothesis is supported by the finding that, in migrating cells, Ag825 decreases HER2 phosphorylation at Y1248, Y1221/2, and Y877 (i.e., inactivates HER2) only after PTPN12 silencing. Conversely, cell exposure to the PI3K inhibitor LY294002 increases HER2 phosphorylation, suggesting the involvement of PI3K/AKT in HER2 regulation. Altogether, the results reveal a new PTEN mechanism in the control cell migration and suggest a complex cross-talk between PTPN12 and HER2.