Abstract Human lymphatic filariasis (LF) is primarily caused by the helminth parasites Wuchereria bancrofti (Wb) and Brugia malayi (Bm). Detecting parasitic circulating cell-free nucleic acids (ccfDNA/ccfRNA) in plasma is a promising approach for detection of active infections. Plasma RNA sequencing analyses from individuals with active Wb infection and uninfected controls identified 6 RNA targets that were specific to Wb and/or Bm. Assays developed to detect either ccfDNA and ccfRNA were successfully used in Wb-infected individuals, but DNA-based assays targeting WbTR1 were found to be the most sensitive biomarker of Wb circulating cell-free nucleic acids. Plasma-derived ccfDNA was identified in 71% (of all microfilaria-positive individuals) of Wb infections from India, the Cook Islands, Mali, Haiti, and Guyana. Following definitive treatment, time course analyses indicated that WbTR1 ccfDNA levels were undetectable within a year. Overall, ccfDNA/ccfRNA detection in lymphatic filariasis holds promise for assessment of infection and treatment response in Wb and Bm infections.