Police were called to she subway that runs under the A62 Castlegate between New North Road Baptist Church and the old technical college building just after 4am today (Sat July 14).
A scene is currently in place as a forensic examination talkes place.
A West Yorkshire Police spokesman said: "The victim is being supported by specialist safeguarding officers,.
"Detectives from Kirklees District CID are carrying out extensive enquiries into the incident.
"Anyone who witnessed anything in the vicinity of the subway between midnight and 4am, or who has any information that could assist the investigation, is asked to contact officers via 101 quoting crime reference 13180345421. Or call the independent charity Crimestoppers anonymously on 0800 555 111."