The aims of this study were to determine the magnitude and duration of fecal viral DNA shedding after diagnosis of feline panleukopenia (FP) in a group of shelter cats using quantitative real-time PCR (qPCR); to assess the utility of a negative point-of-care test or the resolution of diarrhea and systemic signs as proxy measures for qPCR positivity; and to investigate patterns of additional enteric pathogens in relation to feline panleukopenia viral shedding duration. Feline panleukopenia virus (FPV) infection in clinically affected shelter cats was confirmed by a commercial qPCR test. Observations were made on days 0, 3, 7, 14 and 21 post-diagnosis. Fecal flotation, FPV qPCR and the canine parvovirus IDEXX SNAP Parvo ELISA (SNAP) test were performed on fecal samples. Forty cats and kittens with confirmed panleukopenia were initially enrolled. Sixteen kittens were sampled until day 14, and 12 were followed to day 21. Median DNA viral copy numbers fell below the diagnostic cut-off by day 7, with 13/16, 6/16, 1/16 and 0/12 testing PCR-positive on days 3, 7, 14 and 21, respectively. The SNAP test was positive in 12/16 kittens on day 0 and only 3/16 on day 3. SNAP test results, diarrhea and systemic signs were inconsistent in relation to qPCR positivity post-diagnosis. Additional enteric pathogens were common. The presence of additional pathogen types was suggestive of a longer PCR shedding duration, but this was not tested statistically owing to the small sample size. These findings suggest that cats should be isolated for at least 14 days after a diagnosis of FP, but that release from isolation after this point is reasonable, in association with a multifaceted infection control strategy. The study findings did not support using SNAP test results, diarrhea or systemic signs as proxy measures for virus shedding.