Anti-inflammatory drugs inhibit inflammation, particularly those classified as nonsteroidal anti-inflammatory drugs (NSAIDs). Several studies have reported that propolis has both anti-ulcerogenic and anti-inflammatory effects. In this study, we investigated the bioactive compound and in vivo anti-inflammatory properties of both smooth and rough propolis from Tetragronula sp. To further identify anti-inflammatory markers in propolis, LC-MS/MS was used, and results were analyzed by Mass Lynx 4.1. Rough and smooth propolis of Tetragonula sp. were microcapsulated with maltodextrin and arabic gum. Propolis microcapsules at dose 25–200 mg/kg were applied for carrageenan-induced rat’s paw-inflammation model. Data were analyzed by one-way ANOVA and Kruskal–Wallis statistical tests. LC-MS/MS experiments identified seven anti-inflammatory compounds, including [6]-dehydrogingerdione, alpha-tocopherol succinate, adhyperforin, 6-epiangustifolin, deoxypodophyllotoxin, kurarinone, and xanthoxyletin. Our results indicated that smooth propolis at 50 mg/kg inhibited inflammation to the greatest extent, followed by rough propolis at a dose of 25 mg/kg. SPM and RPM with the dose of 25 mg/kg had inflammatory inhibition value of 62.24% and 58.12%, respectively, which is comparable with the value 70.26% of sodium diclofenac with the dose of 135 mg/kg. This study suggests that propolis has the potential candidate to develop as a non-steroid anti-inflammatory drug.