The documents containing personal information on 45 children were taken during a break-in at the home of a member of staff from the education welfare service at Edinburgh City Council.
The files, which had been missing for more than a fortnight, were said to have been recovered in a car which appears to have been used in the robbery.
The staff member who had been in charge of the files had been working with problem pupils with a poor attendance record and had taken the information home prior to the theft last month.
The files related to pupils at Broughton High School, Granton Primary and Forthview Primary who have had contact with the education welfare service.
Most of the files related to pupils attending Broughton High School, although some were on younger children at Granton and Forthview primaries.
Parents of those whose personal details were taken were contacted about the incident, and education chiefs were trying to determine whether or not the member of staff was allowed to take the work home.
The parents have been informed of the recovery, and the council said the files were “predominantly” about school attendance.
An Edinburgh City Council spokeswoman said: “We recovered the files on Wednesday after we found the car that had been used in the robbery.
“The files do not appear to have been tampered with and we have sent a letter out to all the families to let them know this.”
The theft led to calls for security procedures around private information handled by the council to be stepped up.
Cameron Rose, education spokesman for the Edinburgh Conservatives and a former police inspector, said: “There needs to be greater control over what kind of work is taken home.
“Increasingly, work is stored electronically and increased security may well be something we should see more of.”
In February, the Evening News revealed that the personal details of 1075 schoolchildren in East Lothian were mislaid after being downloaded on to a private memory stick.
Although the file was password protected the actual text on the device had not been encrypted, which East Lothian Council said was in “clear breach” of council IT policy and led to the official being suspended.
The same local authority also accidentally published licensing applications, which included personal details and criminal convictions of taxi drivers, on its website in 2010.