The Football Paper unexpectedly ceased publication on Sunday to be replaced by the Non-League Paper.
The move comes seven months after the title was rescued and relaunched by a new owner.
The Non-League paper had been coming out as a supplement within The Football Paper – which covered all the football leagues.
But on Sunday, The Non-League Paper has returned as a stand-alone publication and The Football Paper did not come out.
In a message to readers on page 2, the NLP said: "The Non-League Paper returns today as a stand-alone publication rather than a pull-out section in the The Football Paper.
"We did our best to maintain the integrity of The Non-League Paper as part of the larger publication.
"And, indeed, many readers enjoyed the larger format. We thank them for their support.
"The Football paper could return next season without the NLP.
"But we recognise that our loyal readers – many of whom have bought the NLP since its launch seven years ago this week – want their own newspaper.
"Now here it is again. And at the affordable price of £1.40."