It shot up from third the previous year, overtaking Jack, which had topped the list for the past 14 years but was relegated to third spot.
A total of 7,549 newborns were given 12 variations of the Prophet Muhammad name last year, such as Mohammed and Mohammad.
The second most popular boy’s name, Oliver, was given to 7,364 babies. Harry and Alfie came in fourth and fifth place respectively.
The official list, which covers all births in 2009 in England and Wales, has Muhammad at number 16 but this does not include the many different spellings, which are all ranked separately.
When they are added in, Muhammad zooms all the way up to top spot for the first time.
In order of popularity, the variant spellings used during the year were: Muhammad, Mohammad, Muhammed, Mohamed, Mohamad, Muhamed, Mohammod, Mahamed, Muhamad, Mahammed and Mohmmed.
There are still other possible spellings but these were not used for births in England and Wales in 2009. Regionally, the single spelling of Muhammad came top of the list for the West Midlands.
Since 1999 the number of babies called Muhammad, however spelled, has increased by more than half. In 1999 the name was given to 4,579 newborns.
Going even further back, the single spelling Muhammad appeared at 73 in the list in 1964 and 87th in 1944.
Overall, the popularity of the most common names has changed little, with the top tens for both boys and girls remaining almost identical.
There were 706,248 children born in England and Wales last year.