Brentford entered the 1958–59 Third Division season full of confidence, after narrowly missing out on promotion in 1957–58. Despite making a profit of £6,789 on the previous season (equivalent to £155,800 in 2019), manager Malky MacDonald decided not to add to his squad and instead planned for the future by bringing in a number of Scottish youngsters. Brentford began the season with a resounding 4–0 victory over Bradford City, hitting top spot, but dropped back after three consecutive defeats. By the time the Bees drew 1–1 with Chesterfield on 4 October 1958, the team's inconsistency could be clearly pointed to a lack of support for forwardsJim Towers and George Francis, who had scored 13 of the team's 17 goals by that point of the season. In response, manager MacDonald paid £6,000 for Luton Town's outside leftGeorge McLeod. Things had to get worse before they could get better and after defeats to Stockport County and Reading in late October, the team recovered and began to perform on a consistent basis.
Brentford had a morale-boosting run to the fourth round of the FA Cup, seeing off Exeter City, King's Lynn and Barnsley on the way to a 2–0 defeat versus First Division club West Bromwich Albion in front of 41,440 at The Hawthorns. The Bees established themselves as promotion contenders after a 6–0 win over Southampton at The Dell on 9 March 1959 (which set a new club record for biggest away Football League win), but Jim Towers' four goals in the victory and total so far for the season of 29 led to a £20,000 transfer bid from Second Division club Sheffield Wednesday, which was ultimately unsuccessful. Three victories and two draws from the following five matches (which included a win and a draw versus leaders Plymouth Argyle) saw Brentford increase their grip on 3rd place in the table, though at a cost to season-ending injuries to Ian Dargie and Len Newcombe. Defeats in crucial matches versus fellow promotion challengers Norwich City and Hull City in early April effectively ended the Bees' promotion charge, but the team won three and drew two of the next five matches (scoring 12 goals and conceding just once), even after the club's hopes of promotion were mathematically extinguished with two matches left to play. The season ended with a 4–0 defeat to 4th-place Norwich City at Griffin Park.
Jim Towers' 37 goals scored in all competitions during the season was just two goals shy of Jack Holliday's club record of 39, set at the same level of football in 1932–33. Towers' strike partner George Francis also finished amongst the top scorers in the Third Division with 22 goals and 24 in all competitions. Brentford finished the 1958–59 season with the best defensive record in the Third Division, conceding only 49 goals and also conceding the fewest away goals (27). A new club record for most league away draws (10) was set during the season and the club record for fewest goalscorers in a season was equalled. The 20 players used in all competitions was the lowest since the end of the Second World War and three players finishing the season as ever-presents in all 50 matches was another post-war record.