Prompt neutrinos due to the decay of charmed mesons produced in the atmosphere from cosmic-ray and atmospheric nuclei interactions may be a significant source of background to ultra-high energy neutrino searches above 10 TeV. We re-evaluate this flux using updated charm production cross-sections based on QCD parameters, the charm quark mass, and the range for the factorization and renormalization scales that provide the best description of this data at fixed target experiments, at RHIC, and at LHC. We find that the prompt neutrino flux is reduced from previous results in the literature by a factor between two and eight, depending on the energy. We discuss the implications of our results for current IceCube data.