Brendan worked in a car auction yard during his time in Sydney in between his increasing golfing commitments and lived with his grandmother while there. He travelled to the US in 1996 to play events such as the Southern Amateur, the Western Amateur and the Porter Cup. He was gaining the attention of national selectors as his game developed further and in 1998, played his way onto the Australian Eisenhower Trophy team, that event staged in Santiago in Chile. The team that year also included Aaron Baddeley, Brett Rumford and Kim Felton.

He would win events such as the Riversdale Cup in 1998 and the Tasmanian Open in 1999, but it was his win at the Australian Amateur in 1999, when he beat New Zealander Mahal Pearce in the final, that convinced him, perhaps more than anything else, that the timing was right to turn professional. "I had won pretty well everything that I could in Amateur golf and if I was to turn pro, then that point was as good as any."

Despite his significant amateur record, Brendan still had to face the Australasian Tour qualifying school at Bribie Island at the end of 1999 and very nearly didn't make it. "I was outside the all important cut off of the top one hundred, which I needed to be in prior to the fourth round to get through to the final two rounds. I shot 69 to get me through and eventually finished 39th."

At his very first start as a professional, Brendan served notice that the adjustment was not going to be too great for him. He opened his professional career with a birdie, par, hole in one, birdie, birdie start at the 1999 Ford Open at Kooyonga in Adelaide to be five under through five holes. He eventually finished with a 69 in his first round and would finish in 45th place in his first event, playing for pay. The very next week he led after round one of the Australian Open at Royal Sydney and was still very much in the hunt into the weekend there. "I think it was the momentum from Adelaide as much as anything else that carried over," he would say. He finished 20th. Brendan made six of nine cuts that season on the Australasian Tour and his professional career was underway.

In 2000 Brendan played a few events in Europe at the completion of the Australasian Tour, mainly on invite. He played the Finnish Masters, the North West of Ireland Open and the Dutch Open making the cut at the Dutch Open. But after a few events, he didn't feel particularly comfortable there, especially at that stage of his career. "I didn't know a lot of the guys and it was a long way from home and not playing well didn't help either. I played the Kirin Open and the Suntory event in Japan that year and felt that Japan might be a good option. I also had encouragement from Alex Mercer to play there so attempted to get my card there at the end of 2000 which I managed to do.