Choi, who was appointed by Mayor Chris Coleman in 2006, also is running for Ramsey County attorney.
His reasons for resigning are to focus on that campaign and to eliminate any perception that personal political motives are behind decisions made in the city attorney's office.
"It's best for me to move on," he said Tuesday.
Choi, 39, wrote his resignation letter Friday, submitted it on Monday and told his staff about his decision on Tuesday. His last day will be April 16.
On April 19, he will become a civil practice attorney for the McGrann Shea Carnival Straughn & Lamb firm.
Coleman said Choi has been an outstanding leader. "In just a few short years he has pioneered innovative efforts to reduce gang violence, streamlined our approach to domestic violence cases and become a national leader in addressing the foreclosure crisis," Coleman said in a statement.
Coleman will make an announcement Wednesday about his replacement plans.