We report a 10-year-old female patient with der(X)t(X;3)(q21.1;q22.1), resulting in 3q duplication and Xq deletion. The main clinical feature was primary ovarian failure and there was no abnormal phenotype corresponding to 3q duplication syndrome. This might be explained by the XIST gene at the X-inactivation center on Xq13.2, which was not deleted in this case. The conventional karyotyping was preliminarily reported as 46,X,inv(X) (q13q26) due to the similar banding patterns of Xq13.2-q24 and 3q25.33-q29. This case highlights the value of using a chromosomal microarray as a clinical diagnostic test for individuals with developmental delay or congenital anomalies.