No one inside the building was injured, but some people in the building were shaken, the El Paso Times reported.
The building's east and west sides are covered by glass windows.
About 4:50 p.m. Tuesday, a bullet penetrated a ninth-floor west side window in the office of Assistant City Manager Pat Adauto. That bullet then went through an interior wall before striking and stopping in a picture frame.
El Paso police spokesman Darrel Petry said investigators do not think City Hall was intentionally targeted but rather was struck by stray shots. Juarez has suffered through a deadly drug cartel war for years.
"It does appear the rounds may have come from an incident in Juárez," El Paso police spokesman Darrel Petry told the newspaper. He said there was a shooting incident at about the same time not far away in Juarez, the Times reported.
-- Lance Murray