The FBI's decision not to recommend criminal charges against her is the greatest example yet that the system is rigged, he told a North Carolina rally.
Democrat Mrs Clinton and Mr Trump are their party's likely choices to do battle for the White House in November.
They are expected to be made the official nominees later this month.
FBI Director James Comey said Mrs Clinton had been careless in how she handled sensitive information but there was no case to bring criminal charges because there was no evidence of intent.
Speaking in Raleigh, Mr Trump disagreed and said the system had been set up to protect the Clintons - she had put the "entire country in danger" and had probably been hacked.
"Her judgment is horrible," he said, adding: "She will be such a lousy president, folks."
The New York businessman also said that Attorney General Loretta Lynch had been bribed, getting a promise she would keep her job in return for allowing Mrs Clinton to escape prosecution.
Other Republicans were also critical of the FBI decision. House Speaker Paul Ryan said it "defied explanation".
"Declining to prosecute Secretary Clinton for recklessly mishandling and transmitting national security information will set a terrible precedent," he said.