To find the best post-harvest processing method for Scutellaria baicalensis Georgi, we explored the effects of fresh and traditional processing on the active ingredients in S. baicalensis and evaluated three drying techniques to determine the optimal post-harvest processing technique. We quantified four active ingredients (baicalin, baicalein, wogonoside, and wogonin) in 16 different processed S. baicalensis samples that were harvested from Tongchuan, Shaanxi province, by HPLC (high-performance liquid chromatography). In addition, we performed a similarity analysis (SA), a hierarchical cluster analysis (HCA), and a principal component analysis (PCA) on the common peaks in S. baicalensis that were identified by the HPLC fingerprints. Compared to the traditional processing method, the fresh processing method could better preserve the four active ingredients in S. baicalensis, meanwhile, the similarity analysis (0.997–1.000) showed that the fresh processing was more similar to the traditional processing, and it did not change the type of 18 active ingredients in S. baicalensis. The cluster analysis results showed that the shade drying and sun drying methods results were more similar to each other, while the oven drying (60 °C) method results were clustered into one category. According to the results of the principal component analysis, S9, S7, and S8 had higher scores, and they were relatively well processed under these processing settings. Fresh processing could be an alternative to traditional processing; the moisture content was reduced to 24.38% under the sun drying condition, and it was the optimal post-harvest processing solution for S. baicalensis.