The Fermi Gamma-ray Space Telescope recently detected the most energetic gamma-ray burst so far, GRB 080916C, and reported its detailed temporal properties in an extremely broad spectral range: (1) the time-resolved spectra are well described by broken power-law forms over the energy range of 10 keV-10 GeV, (2) the high-energy emission (at ε > 100 MeV) is delayed by ≈5 s with respect to the ε 1 MeV emission, and (3) the emission onset times shift toward later times in higher energy bands. We show that this behavior of the high-energy emission can be explained by a model in which the prompt emission consists of two components: one is the emission component peaking at ε ∼ 1 MeV due to the synchrotron-self-Compton radiation of electrons accelerated in the internal shock of the jet and the other is the component peaking at ε ∼ 100 MeV due to up-scattering of the photospheric X-ray emission of the expanding cocoon (i.e., the hot bubble produced by dissipation of the jet energy inside the progenitor star) off the same electrons in the jet. Based on this model, we derive some constraints on the radius of the progenitor star and the total energy and mass of the cocoon of this GRB, which may provide information on the structure of the progenitor star and the physical conditions of the jet propagating in the star. The up-scattered cocoon emission could be important for other Fermi GRBs as well. We discuss some predictions of this model, including a prompt bright optical emission and a soft X-ray excess.