Tree peony (Paeonia suffruticosa Andr.), a species native to China, is one of the most important ornamental and medicinal plants. Like other tree species in temperate and boreal zones, the dormancy-activity transition of floral buds is critical for blooming time and fruit production. However, floral buds contain high levels of secondary metabolites, making the isolation of high quality RNA difficult. To obtain a method suitable for extracting RNA from floral buds of tree peony, we evaluated five different methods, including the cetyltrimethylammonium bromide (CTAB) and Sodium dodecyl sulfate (SDS)-based methods, a modified SDS-TRNzol protocol, and two commercial kits (TRNzol and Qiagen RNeasy Plant Mini Kit). The modified SDS-TRNzol method was capable of efficiently removing polyphenols and other metabolites in floral buds. The isolated RNA was of high purity and integrity, as demonstrated by the the A 260/280 ratio of approximately 2.0, and RIN values of more than 9.0. Gel electrophoresis analysis indicated that the extracted RNA had clear 28S and 18S ribosomal RNA bands without DNA contamination. The RNA isolated by this protocol was successfully used for downstream manipulations, such as RT-PCR, RACE, and real-time PCR. Together, the modified SDS-TRNzol protocol is an easy, efficient, and highly reproducible method for RNA isolation from floral buds rich in secondary metabolites.