Speaking to reporters at the Monaco Grand Prix, the American was confident there would be a return to The Brickyard but the post-mortem into what went wrong this year was still being carried out.
Brown said the reasons why McLaren felt they should be at Indianapolis had not changed and highs and lows were part of the sport.
"I think you have to dust yourself off, learn by your mistakes and come back fighting. So that's what we intend to do," he said. "To not do something is easy but that's not what winners do.
"There's very good reasons why McLaren should be in Indianapolis, it's a big market and partners want to be there. Our motor business is strong there."
Spaniard Alonso, a double Formula One champion and Le Mans 24 Hours winner who is chasing the so-called 'Triple Crown of Motorsport', failed in regular qualifying and then finished fourth in a shootout for the last three grid positions.
A list of errors made by the team emerged subsequently, from having to scrounge a steering wheel at short notice to missing vital track time because the spare car was the wrong shade of orange and was elsewhere being resprayed.
Mechanics even confused inches with centimetres.
Brown said there had been "a lot of mistakes that snowballed".
Bob Fernley, the man in charge of the McLaren Indy programme, left immediately after the failure but Brown said that "ultimately it was a people issue, starting with myself, of not having all the bases covered and we just were unprepared.
"I got a variety of my decisions wrong. I think it would be unfair to blame Bob for us not qualifying. I put that on me because I put the team together."
He said he had not wanted to cover anything up but some context was needed.
"It's not like we showed up to the test and went 'someone forgot the steering wheel'," he said. "We were going to do our own steering wheel and we didn't get it done in time. And you need a steering wheel.
"At Cosworth you can buy them off the shelf, they didn't have any on the shelf. And so I had to pull some favours and (partners) Carlin helped to get us a steering wheel."
After qualifying was over, there was talk about possibly buying Alonso a place with another team but that was not felt to be the right thing to do.
"When we do it again, I'll make sure I've got all the right people in the right places," said Brown, adding that the decision to continue would be independent of Alonso's future.
"We were never doing Indianapolis for Fernando," he said. "Whether Fernando wanted to drive with us or not wouldn't drive our decision on whether we go back to Indy or not."
(Reporting by Alan Baldwin, editing by Toby Davis)
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