The Midland Great Western Railway opened the Manulla-to-Foxford line on 1 May 1868, and extended it to Ballina five years later. The branch to Killala opened on 2 January 1893 under Balfour's Light Railways Ireland Act. The whole network existed largely to move agricultural produce east to Dublin and onward to British markets. In 1920 the station reported that it was sending almost nine hundred cases of eggs each week toward English breakfast tables. Thousands of seasonal agricultural labourers, called migratory workers, travelled from Ballina by rail to Dublin and then by ferry to England to help bring in the harvest. The trains carried more than freight. They carried entire summers of human labour, year after year, from the impoverished west of Ireland to the wheat fields of Lincolnshire and Yorkshire.

In December 1906, after a busy market day, the booking office of Ballina station was holding more cash and cheques than usual. A few days earlier, a runaway car had crashed into the building and broken a window, which had been temporarily replaced with a wooden shutter. The thieves removed the shutter with a crowbar, climbed in, and dragged out a safe weighing 1.5 hundredweight containing £127. They smashed it open with a blacksmith's sledge and an iron pin which they left behind in a field. A few days later, two former Ballina residents, Dennis Callaghan and James McGinty, were arrested in a Derry boarding house with most of the money. Both pleaded not guilty. Both were convicted. Callaghan, who had previous form, got five years' penal servitude; McGinty got eighteen months. The booking office got a new window. The story became local legend, partly because the thieves had thought of so much and forgotten about fingerprints.

The station was always a target during the Irish revolutionary period. In July 1920, during the War of Independence, armed men held up the night watchman at gunpoint and stole a consignment of steel shutters destined for Royal Irish Constabulary stations, presumably to deny the police their bullet-resistant windows. In February 1923, during the subsequent Civil War, National Army soldiers arrested two young women at the platform as they tried to board a train for Dublin. The women, identified as Miss Jeanie McInerney and Miss Moore, were described in the press as 'organisers for the anti-Treaty party' and were carrying a number of 'important dispatches' and a large sum of money. They had used the station the way countless others had: as a place where you could get on a train and disappear into the country. The station kept witnessing political history, then opening its doors again to the next train.

During the Second World War, when coal imports were impossible, the Irish state turned to peat. Bord na Móna, the state turf board, had been founded in 1934 specifically to develop the bogs as a domestic fuel source. By 1942, Mayo County Council reported that Ballina station was receiving up to forty trucks of fuel a day from the bogs of Mayo, all destined for the kitchens, power stations, and factories of Dublin. The country was officially neutral in the war but desperately short of everything. The railway became a lifeline, hauling literal fuel to the capital, while many of the families who had cut the turf got nothing in return except the wages of their labour. The trains ran. The country ate. The cities heated their homes. The war ended.

On 23 May 2023, Ballina station marked its 150th anniversary with a small ceremony. Dara Calleary, the local TD and Minister of State, was there, along with the station manager Matthew Garrett and two former station managers, Tommy May and Pat Hopkins. They cut a commemorative cake. The station today is a single platform with a runaround loop. The second platform and the original MGWR signal cabin were demolished in 1977 to make room for freight facilities. The booking office that was robbed in 1906 has been rebuilt several times since. Iarnród Éireann still runs passenger trains here three times a day, and Ballina is one of Ireland's major rail freight hubs, with timber bound for Waterford Port and other goods for Dublin. The migrants stopped leaving from this platform decades ago. The freight keeps moving.