Longer journey times during off-peak periods cost £5.6 million in the first year, compared with shorter journeys at peak periods which had a benefit worth £5.1 million.
Nearly half of the schemes with an objective to cut journey times failed to achieve that goal.
The location of projects which resulted in increased congestion with the most expensive economic costs include the junction of the A5 and A49 in Shrewsbury at £2.5 million.
Highways England published the figures in a recent report after evaluating the first-year impact of nearly half of the 119 schemes, which were carried out on England's motorways and major A roads.
It believes the negative impacts were predominantly caused by the introduction of traffic lights.
A spokesman for Highways England said: "This report shows that overall, these schemes were successful at tackling congestion at the busiest times and improving safety.
"This useful insight is helping us develop improved appraisal methods for small-scale schemes, which in turn help us deliver improved benefits to people using our motorways and major A roads.
"Meanwhile, we are considering a range of options to improve journeys by using traffic signals which respond to traffic flows."
The report concluded that it must consider the impact of projects "across all 168 hours of the week, not just the 10 to 30 peak hours".
Future schemes must "better consider how to mitigate the downsides while maintaining the upsides", the document added.
But the RAC described the findings as "very disappointing".
RAC head of roads policy Nicholas Lyes said: "While congestion has been reduced at peak times of the day, unfortunately many schemes have seen increased traffic at off-peak periods, mostly due to traffic lights being introduced.
"Luckily, it seems as though there are some simple steps that can be taken to improve the worst of these new off-peak traffic flow issues, such as changing signals to work part-time instead of full-time.
"It is also important to realise that this work was not just about reducing congestion and that many schemes have seen small reductions in the number of road casualties."
Other schemes that saw increased traffic include the M6 junction 23 in Newton-Le-Willows, Merseyside, and the M40 junction 9 in Wendlebury, Oxfordshire.