Syphilis is a Sexually Transmitted Infection (IST) with significant importance to public health, due to its impact during pregnancy (Gestational Syphilis—GS); especially because syphilis can affect fetus and neonates’ development (mother-to-child transmission—MTCT of syphilis), by increasing susceptibility to abortion, premature birth, skeletal malformations, meningitis and pneumonia. Measures to control and eliminate MTCT of syphilis have failed on the last few years in Brazil and this research aimed to identify the seasonality of notified cases of syphilis in a region of São Paulo state. The studied region, Pontal do Paranapanema, comprises 32 cities located in the West of São Paulo state, in Brazil. Data collected from the National System of Aggravations and Notification (SINAN) website was used to calculate the incidence rate of GS and MTCT. The incidence rate of GS was acquired dividing number of cases by number of women in each municipality and MTCT using number of live births in each year (from 2007 to 2013) in each municipality. This result was then, standardized multiplying incidence rate by 10,000 and expressed as incidence/10,000 women or live births, for GS and MTCT, respectively. To identify possible endemic/epidemic periods, a control diagram was performed using the standard deviation (SD) of incidence rate. Thematic maps representing the spatial distribution of incidence rates were constructed using a Geographic Information System software (GIS, based on cartographic vector available on the Brazilian Institute of Geography and Statistics (IBGE) website. Eighty cases of GS and 61 cases of MTCT were notified in the studied region. An increase of GS notification was detected in the Pontal do Paranapanema in 2011 followed by an increase in number of MTCT cases in the subsequent year, suggesting inefficacy in the treatment during gestational period. Most of those cases were reported on February and November which suggested seasonality for this IST in the region. The control diagram, based on the inputs collected from SINAN, showed no endemic period; however, the most susceptible month to happen an endemic event of GS and MTCT was February. Our study provided a new methodology to understand the syphilis dynamics as a potential tool to improve the success of future measures to control and possibly eliminate MTCT of syphilis.