The Iron were beaten 3-0 by Blue Square Premier leaders Aldershot Town to bow out of the competition at the third round stage, having pocketed £20,000 in prize money from their run.
Braintree boss Lee Patterson felt Aldershot were the better side and had no complaints about the outcome of the tie.
He said: "I am philosophical about it and there was a difference between the two sides in terms of fitness, as they're a full-time side.
"We got punished for our mistakes and the higher you get in football, the more costly they can be.
"It's disappointing but we came up against an exceptionally good Aldershot side and we have had a good run in the FA Trophy."
After a quiet opening, Braintree were clinically punished by the Shots after 16 minutes.
Midfielder Robbie Martin gave away possession, allowing Aldershot's John Grant to break through the defence and drill a shot past goalkeeper Nicky Morgan, off the post.
Aldershot edged proceedings before the break but the Iron, watched by more than 200 supporters who had made the trip from Essex, only trailed by a single goal at half-time.
Striker Chris Sullivan replaced the injured Andy Porter and Braintree enjoyed their best spell of the tie in the opening ten minutes of the second half.
Sullivan and captain Bradley Quinton both created chances - but it was the Shots who went further ahead.
A clearance from the Iron defence fell to Ben Harding, whose 25-yard drive flew into the top corner.
Sullivan was desperately unlucky not to pull a goal back for Braintree when he broke down the left and unleashed a shot which struck both the crossbar and post.
However, the Shot's superior fitness told during the latter stages.
And they wrapped up their victory with three minutes remaining through Grant, who scored from close range after Scott Davies had intercepted Russell Edwards' pass, to leave Braintree to concentrate on their Blue Square South campaign.
Reporter: Jon Waldron
Source: http://www.braintreeandwithamtimes.co.uk/