She worked as a senior scientist for Strategic Analysis, Inc. which provided support to DARPA. She provided support and oversight of the Spintronics, Quantum Information Science and Technology (QuIST) and Molecular Observation and Imaging programs. She worked at the United States Naval Research Laboratory for 4 years in the laboratory for computational physics and fluid dynamics. Chtchelkanova joined the National Science Foundation in 2005. She is a program director in the Division of Computing and Communication Foundations and oversees programs involving high performance computing.