​Olney would have remained a wayside station on a not particularly important branch line were it not for the opening of the Stratford-upon-Avon, Towcester & Midland Junction Railway (formerly the Easton Neston Mineral & Towcester, Roade & Olney Junction Railway) from Towcester to Ravenstone Wood Junction on the B&NR on 13 April 1891. At Towcester the line joined the East & West Junction Railway which ran through Woodford (where from 1899 it was linked with the London Extension of the Great Central Railway) At Fenny Compton it crossed the Great Western main line running north from Banbury, to which it was linked only by a reverse crossing, and continued through Stratford-upon-Avon (where there was a junction with the GWR line towards Birmingham) to Broom Junction on the Midland Railway. At Towcester the line was joined by the Northampton & Banbury Junction Railway from Blisworth, which continued from a junction at Greens Norton to Cockley Brake Junction on the L&NWR's route from Bletchley through Buckingham and Brackley to Merton Street station in Banbury. From 1908 the E&WJR enjoyed the charismatic leadership of Harry Willmott (1851-1931), as chairman, and his son Russell Willmott (1879-1920), as traffic manager. In 1910 the Willmotts brought about the merger of the ST&MJR with the E&WJR and the N&BJR to form the Stratford & Midland Junction Railway, which became part of the LMSR in 1923, and of British Railways after nationalisation in 1948. When Russell Willmott left to manage the Isle of Wight Central Railway in 1912 it was remarked that he and his father had raised the SMJR from a poverty-stricken company to one with a Two and a half per cent dividend, and that 'no day was too long for him'.

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The E&WJR and the ST&MJR both had links with the Midland Railway, which included running powers over the Three and a half miles from Ravenstone Wood Junction to Olney. As soon as the line opened the Midland began to work freight trains from Bristol through Broom Junction, where they had to reverse, to Olney and thence through Bedford to Somers Town. Initially these trains were powered by Midland locomotives but when they proved too heavy E&WJR locomotives were used from 8 December 1891. It appears that most trains in the Towcester direction were banked out of Olney as far as Ravenstone Wood Juction.

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The ST&MJR and SMJR were able to use the station and other facilities at Olney. The Midland Railway built a small running shed, opened in 1892, with a water tank on its roof and a 50 ft turntable. The shed was formally closed by the LMSR in 1928, which probably meant that it no longer had an allocation of locomotives or permanent staff, but its facilities continued in use until the late 1950s, probably because engines were usually changed at Olney on through trains between the SMJR and London.

A passenger service between Towcester and Olney over the ST&MJR began on 1 December 1892, but it was not well-supported, taking only Five pounds sterling in revenue in some weeks, and it ceased on 30 March 1893. From that date the only passenger trains using the section between Olney and Towcester were special workings, particularly excursions to the Easter Monday race meetings at Towcester. In the 1930s there were also special trains to Stratford from places on the Midland Division of the LMSR, and occasional excursions from Stratford to Southend. The ST&MR was linked at Roade to the main line of the L&NWR by a spur opened on 13 April 1891 which remained in use only until 24 May 1917 although the bay platform on the down side of Roade station never used for passenger trains,was not filled in until 1936.

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The Midland Railway supposedly ceased using the SMJ line for through freight workings in 1913, but overnight goods trains from Broom Junction were still scheduled in the working timetable of October that year, with eastbound workings arriving at Olney at 00.47 and 02.53. A freight train from Woodford was due at Olney at 00.03. The Railway Magazine remarked in 1924 that the MR's banana trains from Avonmouth to London via the SMJR had run 'for many years past'. The LMSR made considerable investments in relaying track around 1928. During the 1930s the line remained open through the night for through freight trains, particularly for the banana workings. Freight trains in the 1930s appear to have been handled by ex-Midland Railway 2F and 3F 0-6-0s from the shed at Stratford-upon-Avon (3256, 3551, 3615, 3677, 3695, 3726 were identified in 1931), together with some ex-Lancashire & Yorkshire Railway 0-6-0s, of which 12105/07/09 were shedded at Northampton in 1930.

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Much remains to be discovered about workings on the line through Olney during the Second World War. Evacuees from London were probably brought to the area by train, although no details are currently known. The wartime ordnance depot at Yardley Chase, accessed from sidings near Piddington station, certainly brought traffic to the line, as did a NAAFI depot at Turvey which consisted of Nissen-type huts close to the station. Further military traffic might have come from the Royal Ordnance Factory at Elstow, south of Bedford, the depot that remains open near Kineton, known in wartime as Marlborough Farm Camp or Burton Dassett and the depot at Ashchurch on the ex-MR Birmingham - Gloucester line south of Broom Junction. Troop trains and some ambulance trains would certainly have passed through Olney. On 29 May 1946 Maurice Jeyes fired 4F 4362 on a special numbered M885 to Byfield. This may have carried German prisoners-of-war from Colchester, one of whom recalled making such a journey in a special train in 1946.

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Nationalisation of the railways in 1948 initially made little difference to workings in the Olney area. Through workings across the SMJR continued. It appears that such trains were limited to 26 loaded wagons westbound, but up to 45 empties were permitted eastbound. These workings probably included banana trains once imports were resumed after the war. A notable event, recorded in several photographs, was a tour of the SMJR lines by officials in an ex-LMSR inspection saloon in June 1950, headed by the 4-4-0 40672 'Engineer Watford'. Photographs taken at Stoke Bruerne and Salcey Forest stations have been published in several collections. The same locomotive also passed over the line with an inspection saloon on 4 October 1944, and on 29 April 1952 a 'district officers' special to Piddington was worked by Stanier 3P 2-6-2T No 40160.

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While the push-and-pull passenger service between Northampton and Bedford in the 1950s was more frequent than at any time in the past, a decline in freight workings was reflected by the singling of the track in 1952. All trains in the Turvey direction used the up line, while the down line was used for carriage storage. A photograph of 1962 shows ex-LMSR non-corridor coaches stored in the sidings at Olney.​