The impact of selection of prescription isodose line (IDL) on plan quality has not been well evaluated during inverse planning (IP). In this study, a total of 180 IP plans at five levels of IDL were generated for 30 brain metastases (BMs). For each BM, one round of IP was performed with typical IP settings, followed by a quick fine‐tuning to ensure the same target coverage and comparable conformality index. The impact of the IDL on the quality metrics (selectivity, gradient index [GI], and treatment time) was evaluated. The decrease of selectivity and increase of GI meant inferior target dose conformality and more dose spillage. Additionally, a metric directly correlated to the treatment time was proposed. For all cases, the mean GI decreased monotonically as IDL decreased from 70% to 30%, and the decreasing rate was significantly different based on tumor size. The mean selectivity and number of shots decreased monotonically as IDL decreased for all the tumors. From 70% to 30% IDL, the decreasing rate of the mean selectivity was 2.8% (p = 0.020), 7.7% (p = 0.005), and 15.4% (p = 0.020) and that of the number of shots was 75.4% (p = 0.001), 73.2% (p = 0.001), and 50.7% (p = 0.009), for the large, medium, and small tumors, respectively. For the medium and small tumor groups, the mean treatment time increased monotonically when IDLs decreased (increasing rate was 80.0% [p = 0.002] for medium tumors [p = 0.001] and 130.8% [p = 0.001] for small tumors from 70% to 30%). For the large tumors, the mean treatment time was the shortest at 50% IDL (59.0 min) and higher at 70% (65.9 min) and 30% (71.9 min). Overall, the GammaPlan chose smaller sectors for plans with lower IDLs except for the large size group.