Torque teno virus (TTV) is a single-stranded DNA virus which is predominantly transmitted by the fecal–oral route and may be excreted in the absence of the clinical symptoms. TTV was previously considered a probable cause of hepatitis, but further studies could not strongly connect TTV to any serious health problem. TTV is highly resistant to water and wastewater treatment processes and can be a useful indicator for determining the fecal contamination of water. The purpose of the present study was to assess the prevalence and molecular characterization of TTV in treated wastewater in Tehran. Thirteen effluent samples were collected monthly from the biggest wastewater treatment plant in Tehran, Iran (from September 2017 to August 2018). The presence of the TTV was monitored in the samples by the nested polymerase chain reaction (PCR) method. The TTV genome was found in 76.9% of the samples, and TTV of groups 1 and 3 were determined using phylogenetic analysis. Therefore, treated wastewater can play a key role in the transmission of TTV and the usage of treated wastewater as a source of potable water needs to be carefully controlled.