This paper presents an impact evaluation of scholarships, within the Brazilian context, on the scientific performance of Ph.D. holders. The objective is to measure the scholarly production of beneficiaries from FAPESP’s (São Paulo Research Foundation) Ph.D. Scholarship Program against unsuccessful applicants. The studied population includes all the individuals who applied for Ph.D. scholarships between 2003 and 2017 and were either granted or rejected by FAPESP. Our evaluation employed a quasi-experimental with ex post facto design. The treatment group comprehends awarded individuals that have completed their Ph.D. degree. The control groups comprehend individuals who: (a) had their application rejected but completed their Ph.D. with scholarships from other funding agencies; and (b) who were rejected but completed their Ph.D. without any scholarship. Additionally, we also conducted an analysis comparing FAPESP awardees with best-rejected individuals. Data collection was carried out for all knowledge fields on large secondary databases (including Scopus and Google Scholar for citations and H-index, Lattes Curriculum Vitae, FAPESP, and CAPES—Coordination of Improvement of Higher Education Personnel). We used exact matching for the analysis. We find that the number of publications, citations, and H-index is higher for FAPESP scholarship holders than for those rejected. The “FAPESP scholarship effect” is much higher when compared to those who did not have support from funding agencies to complete their Ph.D. studies. Therefore, our results vindicate the importance of scholarships for doctoral students to produce qualified scientific knowledge in an emerging economy like Brazil.