A navigation tool holder for a mobile device can include a top holder, a bottom holder, and a cover layered on top of the top holder. The top holder defines an opening for receiving a navigation tool. The bottom holder is configured to matingly engage the top holder. A navigation tool housed between the top holder and the bottom holder. The navigation tool includes a top portion protruding through the opening of the top holder and a flexible circuit communicatively coupling the navigation tool to a circuit board of the mobile device. The cover layer on the top holder can surround the top portion of the navigation tool so that the cover maintains an alignment of the navigation tool with a housing of the mobile device.