With a whole new team of players following the arrival of Stimson, Stevenage started the season slowly, winning just one league match in their opening nine fixtures. As the season progressed, Stevenage started to hit form, winning ten leagues matches out of thirteen from November 2006 to March 2007, propelling them to just outside the play-off places. However, a patchy end of season run meant that the club finished the campaign in eighth place, eight points behind the final play-off position.
Despite missing out on the opportunity of promotion, the season will be remembered for the club's FA Trophy success — winning the competition for the first time in the club's history, courtesy of a 3–2 victory against Kidderminster Harriers at the new Wembley Stadium. The contest was the first competitive match, and final, to be played at the new ground. Stevenage had trailed 2–0 at half-time, before scoring three second-half goals to win the competition in-front of a record crowd of 53,262. The club also competed in the FA Cup, but exited at the First Round stage after losing to league opposition in the form of Wrexham.Steve Morison, a signing from Bishop's Stortford at the beginning of the season, was the club's top goalscorer, scoring 34 goals during the season, with 24 coming in the league, two in the FA Cup, and eight en route to their FA Trophy victory. Stevenage captain Ronnie Henry, who became the first player to lift a competitive trophy at the new Wembley Stadium, was named as Player of the Year for the season.
Stevenage Borough entered the 2006–07 FA Trophy at the First round stage, facing Merthyr Tydfil at Broadhall Way. Stevenage won the game 7–0, their biggest victory of the season, with George Boyd scoring four of the goals — three of which were scored in four second-half minutes. Goals from Steve Morison, Steve Guppy and substitute Craig Dobson completed the scoring. The club were drawn another home tie, to be played on 13 January 2007, this time against Leigh RMI. The visitors took the lead in the first-half, but Stevenage replied with three goals, one from Jamie Slabber and two from Steve Morison, to win the match 3–1. Stevenage then faced a Conference National side in the form of Morecambe, with the game being played on 2 February at Christie Park. Steve Morison gave the away side the lead in the first-half, finishing from an acute angle. Morecambe equalised in injury-time of the second-half, Garry Thompson netting from the penalty spot to ensure the tie went to a replay. Four days later, the teams faced each other in the replay, played at Broadhall Way. Stevenage won the game 3–0 after the game had gone to extra-time. Steve Morison, with his fifth of the competition, Jon Nurse, and Adam Miller scored Stevenage's goals. Another 3–0 victory followed in the quarter-final of the competition, with Stevenage beating Conference South leaders Salisbury City. Daryl McMahon's deflected effort gave the hosts the lead, before Morison and Nurse rounded off the scoring.
The victory meant that Stevenage would play Grays Athletic in the semi-final, to be played over two legs. The first leg took place on 10 March, with Grays hosting Stevenage at the New Recreation Ground. The game ended 1–0 to Stevenage thanks to a Santos Gaia header in the second-half. A week later, the second leg took place at Broadhall Way. An Alex Rhodes goals four minutes into the second-half tied the scores at 1–1 on aggregate, with the game going to extra-time after Stevenage goalkeeper Alan Julian made a number of saves to keep Stevenage in the game. Stevenage scored seven minutes into extra-time through a Mark Hughes free-kick that evaded everyone — meaning Stevenage led 2–1 on aggregate. Steve Morison netted his seventh of the competition in the 120th minute to seal Stevenage's victory and ensure the club would be participating in the first competitive final at the new Wembley Stadium.
The win meant that Stevenage would face Kidderminster Harriers at Wembley Stadium on 12 May 2007 — with Kidderminster beating Northwich Victoria 4–3 on aggregate in their respective two legged semi-final. Stevenage won the final 3–2 in front of a record crowd of 53,262, coming back from two goals down to win courtesy of three second-half goals. Kidderminster took a two-goal lead into the interval, both of the club's goals coming from James Constable. Six minutes into the second-half, Mitchell Cole scored from just inside the area after Steve Morison had headed the ball down. Substitute Craig Dobson levelled the scores with fifteen minutes remaining when he toe poked the ball past onrushing keeper Scott Bevan. The comeback was complete with just two minutes left; Morison's initial volley was saved by Bevan, but he reacted fastest to score the rebound and ultimately ensure Stevenage won the FA Trophy for the first time in their history. The victory over Kidderminster in the final meant that Stevenage were the first team to win a competitive trophy at the new Wembley Stadium, with Ronnie Henry the first captain to lift a trophy at the stadium.