Brendan had a good first season in Japan in 2001. He made 11 of 21 cuts and finished 50th on the money list which, considering the adjustment required, was a very solid first season. He was number one in driving distance that year in Japan, ensuring a fan support base from very early on.

He continued to play the Australasian Tour during the Japanese winter, but without a lot of success. It was not until he returned to Japan in 2002 that things really started to fall into place. A good solid start to the year saw him produce several reasonable finishes, but it was when summer arrived that Brendan seemed to find another gear. He reeled off a series of great finishes from July onwards, including his second place at the Sun Chlorella event, where he was beaten in a playoff by Christian Pena, and culminating in his win at the Philip Morris K.K. Championship in October. The Philip Morris was his first win as a professional and he chose a significant event for his maiden win. The tournament was the equal richest in Japan that year and catapulted him to 8th place on the 2002 money list.

Better was to come in 2003 however with this time a win at the Sun Chlorella tournament and a series of consistent finishes seeing him finish in 6th place on that season's Japan Golf Tour money list.
Brendan returned to Australia still searching for that good performance at home and that would eventually come in early 2004 when he finished runner up to Euan Walters at the Jacobs Creek Open. The very next week he was again runner up at the New Zealand PGA at Clearwater in Christchurch, this time behind Gavin Coles. These events were co-sanctioned by the Nationwide Tour and therefore, by virtue of these performances, he would automatically gain access to Nationwide Tour events in the US if he so chose. While all this was going on he also found the time and the game to qualify for the British Open, which he achieved via the Australian version of the International Final Qualifying at Kingston Heath in January of 2004.

There was still further business to attend to in Japan however, winning there in his second event of 2004 on the Japan Golf Tour at the Tsuruya Open and following that with a fourth placing at the Crowns in Nagoya. Two weeks later he was 14th at the Japan PGA and headed straight to the US and the Nationwide Tour to try and capitalise on the hot start to that he had made earlier in the year in Australia and New Zealand.