"We can't allow men who work defending our citizens to continue to lose their lives," Orduna said on Friday.
"That is why I am presenting my permanent resignation."
Franc Contreras, Al Jazeera's correspondent in Mexico City, said Orduna was forced to step down because of the increasing power of drug cartels in the city.
"Juarez, south of Texas, is an important route for the transportation of heroin, cocaine and marijuana.
"The city was the number one spot for drug-related murders in all of Latin America last year, and Orduna's resignation comes as a direct response to the threat, in an effort to save his own men.
"It sends a very strong message to security forces in Mexico that if you don't do what the drugs gangs say, you are taking tremendous risks."
Jose Reyes, the mayor of Juarez, insisted earlier on Friday that the city would not back down in the face of threats.
"We will not allow the control of the police force to fall in the hands of criminal gangs," he said.
But Orduna said he didn't want to endanger more officers.
A retired army major, Orduna took over as chief in May after his predecessor, Guillermo Prieto, resigned and fled to El Paso after the killing of his operations director.
For Orduna's protection, the city built his bedroom at the police station so that he did not have to go home. He also travels in different vehicles when he does go out.