Background: Dengue in some regions has a bimodal seasonal pattern, with a first big seasonal peak followed by a second small seasonal peak. The factors associated with the second small seasonal peak remain unclear. Methods: Monthly data on dengue cases in the Philippines and its 17 regions from 2008 to 2017 were collected and underwent a time series seasonal decomposition analysis. The associations of monthly average mean temperature, average relative humidity, and total rainfall with dengue in 19 provinces were assessed with a generalized additive model. Logistic regression and a classification and regression tree (CART) model were used to identify the factors associated with the second seasonal peak of dengue. Results: Dengue incidence rate in the Philippines increased substantially in the period 2013–2017, particularly for the regions in south Philippines. Dengue peaks in south Philippines predominantly occurred in August, with the peak in the national capital region (NCR) (i.e., Metropolitan Manila) occurring in September. The association between mean temperature and dengue appeared J-shaped or upside-down-V-shaped, and the association between relative humidity (or rainfall) and dengue was heterogeneous across different provinces (e.g., J shape, reverse J shape, or upside-down V shape, etc). Relative humidity was the only factor associated with the second seasonal peak of dengue (odds ratio: 1.144; 95% confidence interval: 1.023–1.279; threshold: 77%). Conclusions: Dengue control and prevention resources are increasingly required in regions beyond the NCR, and relative humidity can be used as a predictor of the second seasonal peak of dengue in the Philippines.