Weather watchers predict more damaging gusts of up to 60mph and the Met Office has a yellow alert in force until lunchtime.
Hundreds were left without power, an HGV was blown over near Wellingborough and trees toppled county-wide by Storm Eunice on Friday.
Experts fear structures already weakened by Eunice could be brought down today causing more travel chaos.
The Environment Agency issued a flood alert for the River Nene between Northampton and Oundle.
Rail passengers are again being warned to check before they travel after services were suspended between Northampton and London on Friday.
Winds are not expected to be as severe as on Friday but local forecasters @NNweather tweeted: “Storm Franklin will impact the county on Monday, particularly through the morning when gusts of 50-60mph are expected.
“The strongest winds are likely for the morning commute or return to school.”
Western Power Distribution, which is responsible for maintaining the electricity supply network, revealed it’s website had 1.8 million hits in two days — around the same number it would normally get in two months.
Operations Director Graham Halladay said: “This has been the worst storm we have ever experienced in our region.
“We have had hundreds of faults, many of them affecting a small number of customers.
“The Met Office has now named Storm Franklin, which is bringing strong winds for the next 24 hours. The worst of the conditions should be to the north of our region but we will be experiencing strong winds, which may cause further issues.”
Network Rail teams will be out monitoring key locations but advises passengers to check National Rail Enquiries before travelling.
London Northwestern Railway, which runs services between London, Northampton and the North West, had to shut down for hours on Friday due to multiple storm-related blockages on the West Coast Main Line.
Fly-away trampolines and a fallen tree caused delays to services in Hertfordshire while wooden pallets blew onto the line near Northampton, causing delays and cancellations.
Lawrence Bowman, LNR customer experience director, said: “The high winds forecast in Storm Franklin risk bringing further disruption to the rail network I urge all passengers travelling on Monday to check their journeys before setting out.”
East Midlands Railway is 'strongly encouraging' passengers from Corby, Kettering and Wellingborough to consider postponing journeys until later on Monday or Tuesday as it expects delays and cancellations.