The year also saw the Strasbourg-based ombudsman open strategic inquiries into key issues, such as the transparency of EU law-making.
She told a committee meeting in Parliament on Monday that reform proposals for the European network of Ombudsmen were launched and also revealed that EU institutions' compliance with her recommendations reached a record 90 per cent.
The Irish-born watchdog presented her annual report for 2015 at a meeting of the petitions committee.
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The Ombudsman investigates complaints about maladministration in the EU institutions, agencies and bodies.
Any EU citizen, resident, or an enterprise or association in the EU, can lodge a complaint with the Ombudsman. The Ombudsman's powers include the right to inspect EU documents, call officials to testify, and to open strategic inquiries on her own initiative.
The Ombudsman investigates complaints about maladministration in the EU institutions, agencies and bodies. Any EU citizen, resident, or an enterprise or association in the EU, can lodge a complaint.
The Ombudsman's powers include the right to inspect EU documents, call officials to testify, and to open strategic inquiries on her own initiative.
O'Reilly said 2015 was "a special year" for the office as it celebrated 20 years of existence.
The office has dealt with 48,840 complaints since 1995.
She told members, "It was special for another reason. It showed how the work of an Ombudsman can have a positive effect over time on the behaviour of the EU administration, in line with my strategy to increase the impact, relevance and visibility of this office.
"By conducting strategic inquiries into problems in EU institutions, my office was able to help raise the already high transparency and administrative standards in EU public bodies still further.
"This was the case across several issues and institutions during 2015. On EU-US trade negotiations, for example, the Commission made great strides in proactively publishing many transatlantic trade and investment partnership (TTIP) documents. It also listed transparency as a basic principle of its new trade strategy, published in October."
She said, "The Commission, in line with my office's recommendations to properly deal with 'revolving door' cases, also started publishing the names and details of certain senior officials who leave the institution to work elsewhere.
"After my contacts with it, the European Central Bank drew up rules on speaking engagements and announced it would publish the meetings of its executive board members, while Frontex accepted my recommendations to ensure that the fundamental rights of migrants who are forcibly returned from the EU are respected.
"My office was often not the sole actor on these issues but was able to channel concerns expressed by citizens, civil society or MEPs by asking EU institutions to take specific steps."
The official went on, "While these results represent systemic gains for citizens, the core of my work remains helping individuals when they encounter problems with EU public administration. I am very happy to note that the compliance rate among the EU institutions was a record 90 per cent in 2014, a full 10 percentage points higher than the previous year.
"The year also saw the launch of reform proposals for the European network of Ombudsmen (ENO), such as conducting parallel inquiries at the national and European level. The proposals, which built on our successful cooperation during the Frontex inquiry, are meant to bring greater benefits to citizens by capitalising on our mutual expertise."
O'Reilly told the meeting she has also written to Commission President Jean-Claude Juncker to present her ideas on making the transparency register the 'central transparency hub' for EU institutions, bodies, offices and agencies.
"I welcome the progress so far on the register, with due credit to the Parliament and Commission as not many member states have a functioning lobbyist register. It now should be strengthened and extended to the Council. To be a truly effective tool, I believe the register should become the 'central transparency hub' for all EU institutions and agencies."