Highly transmissible infections with short serial intervals, such as SARS-Cov-2 and influenza, can quickly overwhelm healthcare resources in institutional settings such as jails. We assessed the impact of intake screening measures on the risk of SARS-CoV-2 outbreaks in this setting. We identified which elements of the intake process created the largest reductions in caseload. We implemented an individual-based simulation representative of SARS-Cov-2 transmission in a large urban jail utilizing testing at entry, quarantine, and post-quarantine testing to protect its general population from mass infection. We tracked the caseload under each scenario and quantified the impact of screening steps by varying quarantine duration, removing testing, and using a range of test sensitivities. We repeated the simulations under a range of transmissibility and community prevalence levels to evaluate the sensitivity of our results. We found that brief quarantine of newly incarcerated individuals separate from the existing population of the jail to permit pre-quarantine and end-of-quarantine tests reduced SARS-CoV-2 caseload 30-70% depending on test sensitivity. These results were robust to variation in the transmissibility. Further quarantine (up to 14 days) on average created only a 5% further reduction in caseload. A multilayered intake process is necessary to limit the spread of highly transmissible pathogens with short serial intervals. The pre-symptomatic phase means that no single strategy can be effective. We also show that shorter durations of quarantine combined with testing can be nearly as effective at preventing spread as longer-duration quarantine up to 14 days.