Resumo. The clinically important viruses in the genus Flavivirus include Zika virus (ZIKV), dengue virus (DENV), and yellow fever virus (YFV). Accurately diagnosing flaviviral infection is challenging, especially in regions where multiple flaviviruses co-circulate. Flavivirus nonstructural protein 1 (NS1) is a glycoprotein of approximately 48 kDa whose presence in patient sera is an early marker of infection. The aim of this study was to select a capture aptamer for flavivirus NS1 proteins capable of binding with high affinity to the NS1 in all medically important flaviviruses, with the goal of applying it in aptamer-based diagnostic assays. Aptamer selection was performed using a variation of the SELEX technique, termed CE‑SELEX, which uses capillary electrophoresis (CE) in the separation step. ssDNA sequences obtained after the third CE‑SELEX cycle were sequenced. Quantitative real-time polymerase chain reaction (qPCR) was used to quantify DNA in affinity and specificity assays. An aptamer (Flav8) with high affinity (Kd = 3.58 nM ± 0.22) was obtained that could bind to the NS1 proteins of YFV, ZIKV, and DENV (serotypes 1, 2, 3, and 4) equally. The Flav8 aptamer, owing to its high affinity and ability to recognize the NS1 of all clinically important flaviviruses, is suitable as a capture aptamer for use in Enzyme-Linked Oligonucleotide Assay (ELONA) sandwiches or similar assays.