The 1949-50 season had ended on a sad note with Vale occupying last place in the league - leaking 110 goals in the process - the first time on the club's history that they had finished bottom of their league. But the Innerleithen men hauled themselves up to mid-table respectability in 1950-51 season, before consistently ending up in the top half for the rest of the decade. A second place behind Eyemouth United was achieved in 1953-54, but the East of Scotland FA declared the season null & void due to a huge fixture backlog. This was the first of three seasons during the 50s that the league was declared unfinished due to fixture backlogs, on each occasion no team was declared as champions. By this time the dominant Hearts & Hibs 'A' teams had left the league, but now-familiar East of Scotland names such as Spartans and Hawick Royal Albert had come on board, along with Ferranti Thistle, who would later go on to join the Scottish League and change their name to Meadowbank Thistle.

After a haul of only two trophies in 29 years Vale made up for it by winning double that in the space of five years during the 1950s. The Border Cup was won in 1954, the King Cup in 1955, the Scottish Qualifying Cup (South) in 1957 and the King Cup again in 1959.

Vale qualified for the Scottish Cup during the 1952-53 season and were drawn to play East Fife, with the Methil side running out comprehensive winners 7-1 at Bayview in front of a crowd of 5,338. At the time of the game the Fifers were top of the Scottish League and although beaten in the following round of the national competition by Airdrieonians, they were still in contention for the championship with a few games remaining, but eventually finished four points behind champions Rangers. In 1954 the format for the Scottish Cup was altered with an all-in draw for the smaller clubs and the Qualifying Cup put back to later in the season and renamed the South Cup. Civil Service Strollers were beaten by Vale 3-2 in Edinburgh in the First Round and in the Second Round Fraserburgh were the visitors to Innerleithen and departed with a Third Round place after defeating Vale 4-0.

The following year a controversial Scottish Cup First Round tie at Whithorn ended in a 4-1 win to the hosts. However, Vale had lodged a complaint with the referee before the match that the pitch was two yards short of the minimum length required. On the Monday morning a phone call from the Scottish Football Association asked for the protest fee of 10/- to be sent as the SFA were treating the complaint as a protest. The protest was upheld and the game was ordered to be replayed at Whithorn the following Saturday. This time the pitch had been marked out at a length of 104 yards, 4 yards more than the minimum. Vale had been well beaten the previous week and the replay proved a disaster as Vale left-half William Stevenson fell on the uneven pitch and dislocated his shoulder in only the fifth minute. With no substitutes in those days Vale had to play out the remainder of the game with 10 men and were thrashed 7-0.

Vale reached the final of the South Cup competition in 1956 and played Duns in a two-legged final. Duns won the first leg 4-0 and although Vale were by far the better side in the second leg, they could only win 2-1, meaning Duns were the victors on aggregate.

In season 1956-57 Glasgow University were the visitors in the Scottish Cup First Round and Vale won 6-1. The Second Round was another home tie against Wick Academy, which Vale again won 7-2. In the Third Round, Scottish League side Albion Rovers were drawn in another home tie. In a hard game the visitors scored in the fifth minute, after which Vale more than held their own and unfortunately missed a second half penalty before a second goal four minutes from time sealed the game for Rovers, leaving Vale to ponder what might have been.

In season 1957-58 the SFA changed the cup set up again, with the Scottish Qualifying Cup (South) reintroduced. Vale made a great start beating St Cuthbert Wanderers 3-1 at Kirkcudbright in the First Round, then Civil Service Strollers 5-2 at Liberton. This was followed by a home Third Round match against Selkirk which Vale won 5-1. In the Semi-Final Vale were held to a 1-1 draw at Victoria Park by Chirnside United, but won the replay 4-3. The final - another two-legged affair - was a local derby against Peebles Rovers. In the first game at Peebles, Rovers won 3-1 after the Vale goalkeeper, local lad A Currie, had to leave the field with an injury. The Vale team that day was; A Currie, W Stenhouse, W McQue, S Charters, I Gourlay, J Baillie, L Notman, J Hogg, E Miller, I Lawrie and L Tait. The Vale scorer was Miller. In the second leg, with goalkeeper Currie's injury ruling him out, untried Edinburgh amateur player John Henderson took over in goal in the only change to the team from the first game. The new goalkeeper made a great save early on in the match and Vale went on to open the scoring, then scored another to level aggregate score with 18 minutes left to play. Vale went on to score another 4 goals to run out 6-0 winners on the day and 7-3 victors overall. The Vale scorers that day were Miller 3, Notman 2 and Hogg. Innerleithen Town Council marked the occasion by giving Vale a civic reception in recognition of their success.

On the 15th of February 1958, Vale were drawn away to Kilmarnock in the 2nd Round of the Scottish Cup. Five buses made the journey from Innerleithen and the attendance of 8,922 remains the largest that Vale have played in front of. It was also the day a two minute silence was observed for the Manchester United Munich Air Disaster which had happened a week earlier, in which 20 of the 44 passengers had been killed instantly and another three losing their lives in hospital during the following days. In moving scenes, the Kilmarnock and Vale players marched onto the pitch side by side and the silence was observed with great dignity. The match was expected to be a comfortable win for Killie and so it proved as they ran out 7-0 winners, but perhaps the happiest person afterwards was the Vale Treasurer, the large attendance yielding a cheque for the tidy sum of £400.

Local lad Lindsay Notman, an outside-right who had featured and scored twice in the Qualifying Cup win fell seriously ill early in 1958. As he had also played for Peebles Rovers, a benefit game was arranged between a Vale/Rovers Select and Glasgow Celtic at Victoria Park in November 1958. The Celtic side was managed by Jock Stein and featured Frank Haffey in goal and also Pat Crerand and John Clark. In an entertaining game Celtic won 2-1 and the proceeds from the game were handed over to Notman who also met all the players.