With rounds of 73, 68, 70 and 73 she finished the championship in a tie for 29th place on four-under-par 284 to earn the Smyth Salver.
This is the second year in a row that Thitikul has claimed the low amateur honour.
Thitikul, last year's inaugural Women's Amateur Asia-Pacific champion, was one of two amateurs to make the cut at the year's final major.
Also playing all four rounds at Woburn Golf Club was Japan's Yuka Yasuda, who earned her place in the field thanks to her victory at the Women's Amateur Asia-Pacific in April.
Yasuda posted rounds of 73, 70, 70 and 77 to finish the championship on two-over par 290 and tied 59th place.
Atthaya, 16, booked a ticket to Worburn with her win at the 2019 Ladies European Thailand Championship in Pattaya -- her second triumph in the Ladies European Tour event.
"It's awesome. I never thought that I would be here again because I needed to win on the Ladies European Tour to qualify into this event. It's awesome to get back here," said the Ratchaburi native. "I had a great time. I just played my game and I really enjoyed every moment.
"This week I hit the ball really well but the final round was a bit of a struggle with my putter but I had a really good time here.
"When I play in professional events, I get real experience and I adapt that to every tournament that I play. I just keep wanting to improve my game."
When Atthaya won the Ladies European Thailand Championship in 2017, she became the youngest ever golfer to win a professional golf event at the age of 14 years, four months and 19 days.
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