In autumn calving dairy herds, treatment of cattle not observed in estrus prior to the breeding season is common. Routinely, a single prostaglandin or a modified Ovsynch (MOFT) protocol are used—without evidence of their relative effectiveness. This study compares the effects on conception, associated timing, and profitability of administering cows with prostaglandin or MOFT treatment. A hundred and ninety-two Holstein-Friesian cows from three herds without an observed estrus within 28-days before mating start date were randomly treated with d-cloprostenol (PGOD) or an 8-day MOFT protocol. The association of treatment and calving-breeding start-date interval (CBSI) on the risk of conception were investigated. Partial budget, sensitivity analysis, and Monte Carlo simulation was used to assess economic performance, identify critical input variables, and explore the effects of input uncertainties on model output. There was a significant association between MOFT treatment and conception during 21 and 84 days after mating start date, compared to PGOD. MOFT treatment was associated with a mean net benefit of £58.21 (sd £19.42) and £27.29 (sd £17.75) per cow for herds with a fixed or variable dry-off date, respectively. The relative profitability of an MOFT protocol is dependent on its effects on barren rate and herd dry-off strategy.