Thomson, considered one of the frontrunning candidates to replace BBC director general Mark Thompson later in the year, submitted claims totalling £1,194.92 from October to December last year.
This compared to just £62.75 claimed in taxis by her boss Thompson over the same period.
Thomson is known for claiming large cab bills, as she submitted claims adding up to £566.76 from July to September, and racked up a massive bill of over £1,700 in the preceding three months.
Other notable entries in figures released by the BBC yesterday include a claim for £1,427.71 on taxis by BBC creative director Alan Yentob and £449.30 on train fares for BBC North director Peter Salmon.
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However, the BBC was quick to stress that overall expenses claims by its top executives were down 9% year-on-year over the three months, with "particular savings on hotels, taxis and flights".
A BBC spokesman said: ''There will always be costs associated with running a large media organisation with bases across the UK and abroad, but we are mindful we are spending public money and will continue to work hard to keep expenditure to a minimum.''
Thomson is among the leading candidates to replace BBC boss Thompson when he steps down in the autumn, particularly as she has acted as BBC deputy director general since Mark Byford stepped down.
Speaking on the BBC's Test Match Special programme last week, BBC chairman Lord Patten confirmed that internal and external candidates for the director general role will be interviewed in June, with an appointment expected in July.
Despite a significant cut expected to Thompson's current salary - £671,000 - for his predecessor, Lord Patten said that people would "crawl over barbed wire" for the high profile job.