They look very similar from the side. The difference is in the width. The '39's used a narrow box like the '37-'38. (45-3/4" wide) The '40-'46 boxes were 48-1/2" wide. The runningboards on a '39 and a '40 are in the same basic location. This means the '40-'46 rear fenders had to be 1-3/8" narrower than the '39 rear fenders to make up the difference in box width. If you lay a '39 rear fender flat on the floor and measure from the floor (box flange) to the top of the fender, it will be approx. 13". Measuring a '40-'46 rear fender the same way will give you approx. 11-1/2". Good used '39 PU rear fenders are very hard to find since they fit the one year only.
Measurements are the easy part, the hard part is finding the '39 rear fenders! I believe about half the "1939" rear fenders I see on ebay are mislabeled '40-'46 rear fenders. This includes the fender currently on there. I would have some questions as to the width of the fender if I was interested in it. It looks narrow to me, but it's hard to tell from pics sometimes.
sorry for grave digging, this may help someone. I bought some 38 parts the other day and included was a pair of rear fenders I knew were 39-46 because of the metal thickness and the lack of the style line around the wheel opening. I compared the passenger side of these new fenders to the 41 passenger fender I had on hand and the difference is very apparent viewed side by side.
