A new and distinct cultivar of blueberry plant named BB06-540FL-12 as described and shown herein. BB06-540FL-12 is a new and distinct low chill tetraploid, as illustrated and described, Southern highbush blueberry (Vaccinium) variety based largely on V. darrowii. It is a productive, very early season ripening variety with high quality fresh market characteristics. It is intended for areas which successfully grow lower chill Southern highbush varieties. BB06-540FL-12 provides well-exposed fruit, an upright bush with a small crown, concentrated ripening, firm fruit and easy detachment. BB06-540FL-12 has an attractive blue color with medium amount of bloom, which is modestly maintained during handling. The flavor is very good with a balance of high sweetness levels and medium acidity. Berries have a crunchy and juicy texture with medium storage ability of 2 to 3 weeks.