Photodynamic therapy (PDT) and photochemical internalization (PCI) are two methods that use light to provoke cell death or disturbance of cellular membranes, respectively, via excitation of a photosensitizer and the formation of reactive oxygen species (ROS). In this context, two-photon excitation (TPE) is of high interest for PCI and/or PDT due to spatiotemporal resolution of two-photon light and deeper penetration of near-infrared light in biological tissues. Here, we report that Periodic Mesoporous Ionosilica Nanoparticles (PMINPs) containing porphyrin groups allow the complexation of pro-apoptotic siRNA. These nano-objects were incubated with MDA-MB-231 breast cancer cells, and TPE-PDT led to significant cell death. Finally, MDA-MB-231 breast cancer cells were pre-incubated with the nanoparticles and then injected in the pericardial cavity of zebrafish embryos. After 24 h, the xenografts were irradiated with femtosecond pulsed laser and the size monitoring by imaging showed a decrease 24 h after irradiation. Pro-apoptotic siRNA was complexed with the nanoparticles and incubation with MDA-MB-231 cells did not lead to cancer cell death in dark conditions, but with two-photon irradiation, TPE-PCI was observed and a synergic effect between pro-apoptotic siRNA and TPE-PDT was noticed, leading to 90% of cancer cell death. Therefore, PMINPs represent an interesting system for nanomedicine applications.