Some fares for long, connecting journeys will be removed from the system as cheaper alternatives exist, in a bid to negate the need for split ticketing to save money.
Single-leg pricing will be introduced for some journeys to make it simpler for passengers to know if they would be better off buying two single tickets or a return.
There are also measures to make ticket vending machines more user-friendly.
The trials are due to start in May on selected routes, including CrossCountry, Virgin Trains' east and west coast services and East Midlands.
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In October, the Commons' Transport Select Committee published a damning report which stated that "unfairness, complexity and a lack of transparency" in rail ticketing have been apparent for at least a decade.
Train companies claim they have been prevented from being more flexible in offering tickets that passengers want because of government rules covering rail fares.
The modification pilot schemes, agreed by rail firms and the Government, are designed to establish what changes are needed to regulations and processes to enable train companies to set simpler fares.
Rail Delivery Group director of customer experience Jacqueline Starr said: "We know customers can find it hard to get the right ticket for their journey due to complex rules and regulations built up by governments over decades.
"There are more than 16 million different train fares, many of which nobody has ever bought. This also makes it more difficult to give passengers the right, simple options on ticket machines.
"Working with Government, we're determined to overhaul the system to cut out red tape, jargon and complication to make it easier for customers to buy fares they can trust, including from ticket machines."
Lianna Etkind, public transport campaigner at the Campaign for Better Transport, welcomed plans to simplify the "horribly complicated" fares system, but called for the introduction of "long overdue" part-time season tickets.
She also urged rail companies to protect station staffing levels, as ticket vending machines "cannot replace trained, visible members of staff".
Rail minister Paul Maynard said: "Rail passengers must be able to trust that they are getting the best possible deal every time they travel, and we are working closely with industry on a set of actions to improve fares and ticketing for passengers over the next 12 months.
"The ticket-buying experience is all too often complicated and hard to navigate and I welcome this initiative.
"We want a more modern and passenger-focused fares and ticketing system which takes advantage of all the benefits of new technology."