The line between Oxford and Didcot Parkway was closed for 16 days while flood prevention work took place at Hinksey.
The tracks at Hinksey run alongside the River Thames and have flooded 11 times in 14 years.
They have been raised 60cm (24in) and culverts have been built to allow water to flow underneath the line.
Replacement buses were used during the period the line was closed.
Oxford Station manager Richard Fry said the improvements would "bring Brunel's railway into the 21st Century".
An £18m project to reduce flooding on a stretch of railway near Oxford has been completed.