A retrospective cohort study was conducted to determine if there is an association between short-acting intramuscular (SAIM) antipsychotics used for acute agitation and length of stay (LOS). Patients with a diagnosis of schizophrenia or schizoaffective disorder who were dispensed at least one dose of a SAIM antipsychotic were divided into groups based on the initial SAIM antipsychotic received once admitted to a psychiatric unit. Electronic records were used to gather demographic information, LOS, and number of injections received during an admission. Cost was calculated from the number of injections received. One-hundred and thirty-six patients were enrolled. When comparing the haloperidol group to the second generation antipsychotic group, there was no statistically significant difference, in LOS 16.98 ± 9.56 days versus 17.59 ± 11.52 days (P = 0.75), respectively. There was a statistically significant difference in both cost and number of injections between groups, favoring the haloperidol group. Ziprasidone was associated with a shorter LOS compared with olanzapine, 13.57 and 19.10 days, respectively (P = 0.026). Patient characteristics should be evaluated when determining an agent for acute agitation. However, because literature indicates second generation SAIM antipsychotics are only noninferior to haloperidol; other factors should also be evaluated; including impact on LOS and impact on hospital resources. This study indicates use of a second generation SAIM antipsychotic for acute agitation is more costly, requires more injections, and was not associated with a shorter length of stay when compared with SAIM haloperidol.