President Cyril Ramaphosa and Gauteng Premier David Makhura spent several hours on a Metrorail train travelling from Mabopane to Bosman stations in Pretoria on Monday.
The journey usually takes 45 minutes.
The two caught the train from Mabopane as part of the ANC's ongoing campaign leading up to the national elections in May.
The train apparently experienced a technical glitch.
Speaking to eNCA, the president said they had been on the train since 07:30 and had been stuck for close to three hours.
"Levels of frustration are quite high, but people surprisingly have been patient, patient because they are hoping the ANC would see what's happening and bring about changes," said Ramaphosa.
He added that he and the premier were inspired to take action and said it was not what they wanted to see.
Ramaphosa said they would bring attention to the "lived reality" of South Africans.
The president told the eNCA reporter that he had not communicated with the Passenger Rail Agency of South Africa (Prasa) yet but said he wanted to hold meetings with senior officials over the issues South Africans experienced daily on the trains.
"We haven't interacted with Prasa yet, but we are going to interact with them at the highest level to make sure that the board chair, the CEO, acting or otherwise, will get to fully understand the level of anger and frustration that is amongst our people here," said the president.
Ramaphosa added that there should be meaningful changes following that meeting.
When he finally arrived at Bosman Station, he told News24 that his trip was good "but long".
The ANC president had a more successful journey on a train last Monday.
He visited Park Station in Johannesburg, where he was joined by secretary general Ace Magashule and party leaders Gwede Mantashe and Paul Mashatile, as they canvassed for support among South Africans who were making their way to school and work, News24 reported.
Leaders during that campaigning also promised commuters that the party would intervene so that trains would run on time.