Mean climatological intra-seasonal (i.e., 30-60 day) oscillations in rainfall (hereafter, CISO) have been investigated using the NCEP/NCAR daily reanalysis and daily rainfall data of 753 stations from 1979 to 2010. The results demonstrate an interesting phenomenon: an out-of-phase relationship exists between the intra-seasonal oscillations (ISO) of rainfall in southeastern China (SEC) and the Sichuan-Chongqing-Shaanxi-Gansu region (CYSG). In particular, strengthening of rainfall in SEC is accompanied by weakening of rainfall in CYSG. The low-frequency oscillation of summertime rainfall in CYSG appears to vary locally, whereas that in SEC appears to propagate in the meridional direction. No zonal propagation of CISO in rainfall was found in either area. The CISO in rainfall in both SEC and CYSG were found to be related to migratory low-frequency circulations that traverse the southeastern part of China. However, the CISO in rainfall in the CYSG are associated with replacement of low-frequency circulations between an anticyclonic ridge and a cyclonic trough northeast of the Tibetan Plateau. Vertical motion facilitates the out-of-phase variations of the CISO in rainfall between SEC and CYSG. Furthermore, examinations of Rossby wave propagation using the Rossby wave theory show that the energy of low-frequency eddies propagates intrinsically westward to CYSG from the middle-lower reaches of the Yangtze River (MLYR), indicating a dynamic relationship between SEC, MLYR, and CYSG in terms of CISO rainfall. This relationship may partly explain the out-of-phase relationship between SEC and CYSG. This out-of-phase relationship is also associated with both the temporal variation of the western Pacific subtropical high and the ridges around Lake Baikal at 500-hPa geopotential height. Phase locking of ISO occurs in East Asian monsoon activity and the contributions of CISO rainfall to total rainfall are non-negligible; therefore, knowledge of the out-of-phase relationship of CISO in rainfall between SEC and CYSG is of great importance for better understanding of the local characteristics of ISO and the mechanisms underlying ISO in rainfall.