The paperless system was introduced at Addenbrooke's and Rosie hospitals in Cambridge in October.
Regulator Monitor said it was looking into the trust's "financial problems" as "it may indicate wider issues with how the trust is run".
Cambridge University Hospital NHS Foundation Trust said it was working closely with Monitor.
Monitor managing director Stephen Hay said the investigation was launched "over financial concerns" and would include "how the trust handled the introduction of a major new IT system".
The trust said it had a predicted deficit, but it was "doing everything possible to improve our financial position, whilst ensuring safe care for our patients".
It was the first in the UK to use Epic's eHospital system, which is used in hospitals in the US.
Nurses access and update patient records using 500 iPod Touch devices and, using its barcode scanner, run tests such as measuring blood pressure.
In December, senior hospital consultants said that its introduction was "fraught with problems".
Monitor has previously taken regulatory action over concerns about the trust's finances between 2013 and July 2014.
A hospital trust's finances are being investigated after it introduced a £200m online patient-record system.