Stroke is a medical emergency responsible of a high number of deaths (5.9 million annually). Post-stroke infections, more concretely pneumonia, are the most common post-stroke complication, producing around 30% of the mortality. Even if their early diagnosis is necessary to start with antibiotherapy in the shortest delay, this is a challenging task for the doctors. Consequently, in order to apply new treatment strategies as soon as possible, the aim of this study was to discover and validate infection biomarkers able to predict the patients that will develop an infection during hospitalization. By using quantitative proteomic approaches and including data of the literature, we highlighted two potential promising risk stratificator markers: neopterin and Serum Amyloid A (SAA). This work has demonstrated that both of them are excellent tools to start antibiotherapy in an earlier stage, leading to a better management of the patients and to an improvement of their associated outcomes.