Dale were beaten 9-0 by the Championship club in the EFL Youth Alliance League North West.
Five first-half goals were followed by four after the break for the Imps.
Academy Manager James Caldwell commented: “We played with three under-16s and one under-15 player against a really good and experienced side.
“Whilst it’s a frustrating result, we can’t skip this part of our journey. It’s something that each newly promoted team experiences.
“We struggled with the age gap, and against a tall, physical Lincoln side, we lacked energy in vital areas.
“Reece Leonard and Rhys Beesley stood out for us in a tough game, but we need to be better as a group.
“We have some new trialists coming in, and we have to make sure we have the right players who not only improve us, but have long-term potential.”
The Youth Team are back in action on Tuesday, when they host Carlisle United in the PDL Cup.
