The highly modified urban matrix becomes an inhospitable environment for many species because the natural vegetation fragments are highly fragmented and often isolated in the landscape. Protected Areas (PAs) located closer or within urban areas may not achieve their goal of protecting local or regional biodiversity. Thus, the proposition of ecological corridors aims to connect the PAs, providing the dispersion of species in anthropogenic landscapes. In this context, this study aimed to evaluate the PAs connectivity in an urban landscape and understand if urban forest fragments can support their connectivity, generating important information for biodiversity conservation and urban planning. For this, we used models based on Graph Theory to assess the functional connectivity among PAs. The focal species used were Atlantic Forest birds. We used the participatory technique to assess their dispersal capabilities, and this information was used to create a resistance surface map. The focal species movement in the landscape was modeled through Graph Theory. This model evaluated the functional connectivity and extracted the least-cost paths between PAs and other forest fragments that designed the urban ecological network. We identified that few PAs are connected in the urban landscape of Sorocaba city and its surroundings and 28 forest fragments that are important to support the connectivity among PAs. Among these, only four fragments are located within a PA. The other 24 forest fragments located outside PAs should be the center of attention for forest conservation and restoration actions, as they can improve the connectivity between the PAs. Our results show that PAs connectivity in urban landscapes depends on incentives for native vegetation conservation on private lands once most of the important forest fragments for the PAs connectivity are located in these areas. In addition, the restoration of riparian zones is important because they compose a great ecological corridor in the urban landscape. Strategies that increase the permeability of the matrix (e.g., increasing green spaces and gardens) and restoring target fragments are also important. Finally, land-use planning, focusing on natural ecosystem conservation and combating urban sprawl, is necessary to promote PAs connectivity in urban landscapes.