Anne Wafula-Strike, of Harlow, told how the disabled loo on a three-hour CrossCountry service from Nuneaton to Stansted last month was out of action.
She said train staff knew of her plight but by the time they reached a station with a disabled toilet it was too late.
CrossCountry said the train involved was only in use because cow strikes had left two other trains out of action.
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The 47-year-old Kenyan-born wheelchair racer is a board member of UK Athletics and has an MBE for services to disability sport.
On the day of the incident - 8 December - she was returning home from a "very positive UK Athletics board meeting".
"They put me on the train and there was a wheelchair assistant there with a ramp," said Mrs Wafula-Strike, who said she was not warned in advance the train's disabled toilet was out of order.
"After half an hour I felt I needed to use the rest room and to my amazement the toilet was boarded up with a sign saying it was out of order.
"I waited for the ticket master to come and she was very sympathetic and said she would get me off at the next stop so I could use the toilet there and then they would put me back on.
"But at that particular station there was nobody on the platform to help me. The next possible platform was Peterborough.
"Between me asking for help and getting to Peterborough I just had to do it, I ended up wetting myself. My dignity was taken away, I was humiliated."
Her MP, the Conservative Robert Halfon, wrote to CrossCountry saying Mrs Wafula-Strike's experience was a "totally unacceptable set of events for the 21st Century".
In his response, the managing director of CrossCountry Andy Cooper said Mrs Wafula-Strike's train had a door defect which had been due to be fixed.
"We would not normally have pressed the train into service but in recent months two of our fleet of Class 170 trains have hit cows which had managed to stray on to the line," Mr Cooper said.
"Both trains were so badly damaged that they have required major repairs and been out of service."
He said Mrs Wafula-Strike would be offered complimentary first class travel tickets by way of an apology.
A Paralympian says she ended up wetting herself on a rail journey because the disabled toilet was out of order.