Chris Grayling, who arrived on stage at the Tory conference this morning seven minutes behind schedule, said changes would be implemented to make it easier for people to claim.
Passengers, once registered on the new system, would not have to repeatedly enter their details every time they want to make a claim.
New operators would also be expected to make greater use of technology, such as mobile phone apps, to inform passengers when they are entitled to compensation.
Labour described the announcement as a "cheap gimmick" and argued it does not tackle the "underlying problems" that lead to delays.
The North West and Yorkshire has seen widespread disruption on its railways this summer as a result of the botched introduction of a new timetable by operator Northern.
Speaking at the Conservative Party conference in Birmingham, Mr Grayling also announced that York's outer ring road would be among the first five schemes to benefit from a £100m fund to improve the country's busiest and most important local A roads.
A new section of the road, which has long been identified as a priority for improving traffic flows in York, is one of the recipients of funds from the Major Road Network fund.
More than 5,500 miles of A roads across England could benefit from the new fund, which is designed to improve connections between towns and cities and support regional economic growth.
During this morning's speech, Mr Grayling reiterated his apology for the chaos caused by timetable reforms this summer.
After noting the number of passengers travelling on the railways has doubled in the last 20 years, Mr Grayling said: "Trains are packed, the network is creaking, passengers experience too many things going wrong.
"We need to look after them when that happens, which is why today I can announce that we will introduce one-click compensation for delays and disruption, making it easier for people to claim compensation."
Mr Grayling defended the Government's spending record on railways and criticised Labour for a lack of investment when in power.
Shadow transport secretary Andy McDonald said: "After eight years of failure on transport, the time for tinkering at the edges is over.
"Rail is in chaos and the Tories' one-click compensation plans are yet another cheap gimmick which does nothing to tackle the underlying problems causing misery to passengers across the country.
"Congestion on major roads has worsened, local roads have fallen into disrepair, the UK is failing on air pollution and we are set to miss the Paris climate change targets."