After a fine start, Tranmere found themselves in front on three minutes when Adam Mekki’s cross found the back of the net via the post on two minutes.
The visitors were however on terms a couple of minutes later after Danny Sparkes' 25 yard pile-driver found the left hand side of Scott Davies’ net, leaving the goalkeeper with no chance.
It seemed the visitors gained momentum from their earlier goal when midway through the first half they found themselves in front after a ball by Sparkes found the feet of Simeon Akinola who fired into net from 10 yards.
Scott Davies made a fine stop shortly after to deny a Michael Cheek header, only for the offside flag to be raised.
Tranmere were finding it difficult to break down a resilient Braintree defence.
A Mekki corner five minutes before half time nearly resulted in a Tranmere goal, only for Ritchie Sutton to slice an attempt wide of Will Norris’ goal.
The visitors then had a chance to make it 3-1 when Akinola failed to latch onto a dangerous Powell cross. At the other end, a James Norwood shot from 12 yards nearly brought Tranmere back on level terms only for Norris to get down well and parry away from danger.
It was a frustrating first half for Rovers fans as Braintree went into the break with the lead.
Rovers got the game underway at the start of the second half, and made one change, which saw Adam Dawson replace Liam Ridehalgh.
Braintree had the first chance of the second half when Jake Powell forced a strong one-handed save from Scott Davies.
On 60 minutes, Tranmere came close to levelling after Adam Dawson’s cross found the head of Andy Mangan, only for his header to fall narrowly over the crossbar.
Tranmere were starting to apply more pressure, but the toughest defence in the league were compact and stood firm. There were shouts for a penalty after Adam Mekki went down under the challenge of Kenny Davies, but referee waved away the claims.
A Matt Hill cross mid-way through the second half was headed wide from 10 yards by James Norwood.
With five minutes of added time, a freekick on the right by Mekki found the head of Sutton but he could only find the roof of the net from eight yards.
A Vaughan cross deep into added time found Mangan who fired wide of the goal as Braintree managed to hold on and claim the three points.
Tranmere: Davies, Vaughan, McNulty, Sutton, Hill, Mekki, Maynard, Jennings, Ridehalgh (Dawson 46), Mangan, Norwood. Substitutes: Turner, Ihiekwe, Kirby, Tomlinson.
Braintree: Norris, Clerima, Habergham, Paine, Fry, Davis, Akinola (Marks 89), Sparkes (Brundle 77), Cheek, Woodyard, Powell (Miles 65). Substitutes: Edgar, Sekajja.
Referee: Adrian Holmes
Yellow cards: McNulty (56), Mangan (60)
Goals: Mekki (3); Sparkes (5), Akinola (24)
Attendance: 4224 (44)