The soft-spoken, well-respected Pedersen, 60, whose retirement after 81/2 years as state highway administrator and 29 years with the agency takes effect June 30, said the decision is personal and does not reflect any policy disagreements with the administration of Gov. Martin O'Malley.
Pedersen oversaw the construction of the replacement Woodrow Wilson Bridge over the Potomac River and the new Intercounty Connector toll road in the Washington suburbs — projects that totaled roughly $2.5 billion each.
Maryland Transportation Secretary Beverley K. Swaim-Staley said Pedersen kept both projects on budget and on time.
"It's a great legacy. I don't think it gets any better than that," she said.
Swaim-Staley said she has asked her deputy, Darrell B. Mobley, to serve as acting administrator. The secretary said she will evaluate candidates within the department before deciding whether to look outside for a replacement.
Swaim-Staley said Pedersen will remain on the agency payroll for the next few months as an adviser on the ICC project, the first phase of which opened this year. The second phase, which will complete the connection between Interstate 95 and the Interstate 270 corridor, is expected to open late this year or early in 2012.
Pedersen was named head of the SHA by Republican Gov. Robert L. Ehrlich Jr. in 2003 but made what appeared to be an easy transition into the administration of O'Malley, a Democrat.
The tall, white-haired administrator was known for steering clear of politics. He said Wednesday that it was important that he and his agency colleagues be perceived as "objective professionals."
Pedersen said his relations with superiors at the Department of Transportation and the State House have been excellent. When O'Malley took office in 2007, he said, he found that he and the new governor took a similar approach to performance management.
"I have nothing but the highest regard for the administration and the secretary," he said.
The administrator acknowledged reports from former employees that a critical legislative audit of his agency's procurement practices — focusing on officials who have since left the SHA — is in the works.
"Yes, there were some things that happened in which I was let down by people," he said. Pedersen said those issues had no bearing on his decision to leave his job.
Raquel Guillory, O'Malley's spokeswoman, said the governor thanked Pedersen for his accomplishments.
"Under his leadership, we saw the completion of significant projects, including the Woodrow Wilson Bridge and part of the ICC," she said. "Those projects alone will have a significant impact on Maryland commuters and travelers for many, many years to come."
In separate interviews, Senate President Thomas V. Mike Miller and House Speaker Michael E. Busch used the same word to describe Pedersen: unflappable.
"It was always a pleasure working with Neil Pedersen," Miller said. "Through my interactions with him on many issues over the years, I found him to be one of the most honest and dedicated public servants I have worked with in state government."
Busch said that when citizens would "yell and scream" during public hearings, Pedersen would always remain a "consummate professional."
During the last several years of his tenure, Pedersen has had to grapple with severe funding shortages as a result of a recession-related drop in revenue. But he said he did not find the budget constraints demoralizing.
"I've enjoyed a great deal trying to figure out how we can produce the greatest value to the taxpayers with the dollars that have been made available to us," Pedersen said. Even with those limits, he said, the state has been able to reduce its number of structurally deficient bridges from 160 to 109 since 2003.
Baltimore Sun reporter Julie Bykowicz contributed to this article.